| Count | Error Message |
|---|
| 58 | This is snippy-core 4.6.0Show full stderrThis is snippy-core 4.6.0
Obtained from http://github.com/tseemann/snippy
Enabling bundled tools for linux
Found any2fasta - /usr/local/bin/any2fasta
Found samtools - /usr/local/bin/samtools
Found minimap2 - /usr/local/bin/minimap2
Found bedtools - /usr/local/bin/bedtools
Found snp-sites - /usr/local/bin/snp-sites
Saving reference FASTA: core.ref.fa
This is any2fasta 0.4.2
Opening 'ref.fna'
Detected FASTA format
Read 2956542 lines from 'ref.fna'
Wrote 702 sequences from FASTA file.
Processed 1 files.
Done.
Loaded 702 sequences totalling 206915596 bp.
Will mask 0 regions totalling 0 bp ~ 0.00%
ERROR: snippy_dirs/10_24SA010_S166_L001/snps.aligned.fa has entry 'NC_024355.1' but ref.fna doesn't. |
| 6 | [04:43:40] This is snippy 4.6.0Show full stderr[04:43:40] This is snippy 4.6.0
[04:43:40] Written by Torsten Seemann
[04:43:40] Obtained from https://github.com/tseemann/snippy
[04:43:40] Detected operating system: linux
[04:43:40] Enabling bundled linux tools.
[04:43:40] Found bwa - /usr/local/bin/bwa
[04:43:40] Found bcftools - /usr/local/bin/bcftools
[04:43:40] Found samtools - /usr/local/bin/samtools
[04:43:40] Found java - /usr/local/bin/java
[04:43:40] Found snpEff - /usr/local/bin/snpEff
[04:43:40] Found samclip - /usr/local/bin/samclip
[04:43:40] Found seqtk - /usr/local/bin/seqtk
[04:43:40] Found parallel - /usr/local/bin/parallel
[04:43:40] Found freebayes - /usr/local/bin/freebayes
[04:43:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:40] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:40] Found gzip - /bin/gzip
[04:43:40] Found vt - /usr/local/bin/vt
[04:43:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 6 | [03:39:26] This is snippy 4.6.0Show full stderr[03:39:26] This is snippy 4.6.0
[03:39:26] Written by Torsten Seemann
[03:39:26] Obtained from https://github.com/tseemann/snippy
[03:39:26] Detected operating system: linux
[03:39:26] Enabling bundled linux tools.
[03:39:26] Found bwa - /usr/local/bin/bwa
[03:39:26] Found bcftools - /usr/local/bin/bcftools
[03:39:26] Found samtools - /usr/local/bin/samtools
[03:39:26] Found java - /usr/local/bin/java
[03:39:26] Found snpEff - /usr/local/bin/snpEff
[03:39:26] Found samclip - /usr/local/bin/samclip
[03:39:26] Found seqtk - /usr/local/bin/seqtk
[03:39:26] Found parallel - /usr/local/bin/parallel
[03:39:26] Found freebayes - /usr/local/bin/freebayes
[03:39:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:39:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:39:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:39:26] Found vcfuniq - /usr/local/bin/vcfuniq
[03:39:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:39:26] Found gzip - /bin/gzip
[03:39:26] Found vt - /usr/local/bin/vt
[03:39:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:39:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:39:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:39:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:39:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:39:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:39:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:39:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 6 | [06:47:49] This is snippy 4.6.0Show full stderr[06:47:49] This is snippy 4.6.0
[06:47:49] Written by Torsten Seemann
[06:47:49] Obtained from https://github.com/tseemann/snippy
[06:47:49] Detected operating system: linux
[06:47:49] Enabling bundled linux tools.
[06:47:49] Found bwa - /usr/local/bin/bwa
[06:47:49] Found bcftools - /usr/local/bin/bcftools
[06:47:49] Found samtools - /usr/local/bin/samtools
[06:47:49] Found java - /usr/local/bin/java
[06:47:49] Found snpEff - /usr/local/bin/snpEff
[06:47:49] Found samclip - /usr/local/bin/samclip
[06:47:49] Found seqtk - /usr/local/bin/seqtk
[06:47:49] Found parallel - /usr/local/bin/parallel
[06:47:49] Found freebayes - /usr/local/bin/freebayes
[06:47:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:47:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:47:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:47:49] Found vcfuniq - /usr/local/bin/vcfuniq
[06:47:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:47:49] Found gzip - /bin/gzip
[06:47:49] Found vt - /usr/local/bin/vt
[06:47:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:47:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:47:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:47:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:47:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:47:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:47:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:47:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 6 | [16:31:25] This is snippy 4.6.0Show full stderr[16:31:25] This is snippy 4.6.0
[16:31:25] Written by Torsten Seemann
[16:31:25] Obtained from https://github.com/tseemann/snippy
[16:31:25] Detected operating system: linux
[16:31:25] Enabling bundled linux tools.
[16:31:25] Found bwa - /usr/local/bin/bwa
[16:31:25] Found bcftools - /usr/local/bin/bcftools
[16:31:25] Found samtools - /usr/local/bin/samtools
[16:31:25] Found java - /usr/local/bin/java
[16:31:25] Found snpEff - /usr/local/bin/snpEff
[16:31:25] Found samclip - /usr/local/bin/samclip
[16:31:25] Found seqtk - /usr/local/bin/seqtk
[16:31:25] Found parallel - /usr/local/bin/parallel
[16:31:25] Found freebayes - /usr/local/bin/freebayes
[16:31:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:31:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:31:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:31:25] Found vcfuniq - /usr/local/bin/vcfuniq
[16:31:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:31:25] Found gzip - /bin/gzip
[16:31:25] Found vt - /usr/local/bin/vt
[16:31:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:31:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:31:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:31:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:31:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:31:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:31:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:31:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 6 | [19:40:12] This is snippy 4.6.0Show full stderr[19:40:12] This is snippy 4.6.0
[19:40:12] Written by Torsten Seemann
[19:40:12] Obtained from https://github.com/tseemann/snippy
[19:40:12] Detected operating system: linux
[19:40:12] Enabling bundled linux tools.
[19:40:12] Found bwa - /usr/local/bin/bwa
[19:40:12] Found bcftools - /usr/local/bin/bcftools
[19:40:12] Found samtools - /usr/local/bin/samtools
[19:40:12] Found java - /usr/local/bin/java
[19:40:12] Found snpEff - /usr/local/bin/snpEff
[19:40:12] Found samclip - /usr/local/bin/samclip
[19:40:12] Found seqtk - /usr/local/bin/seqtk
[19:40:12] Found parallel - /usr/local/bin/parallel
[19:40:12] Found freebayes - /usr/local/bin/freebayes
[19:40:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:12] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:12] Found gzip - /bin/gzip
[19:40:12] Found vt - /usr/local/bin/vt
[19:40:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 6 | [14:44:49] This is snippy 4.6.0Show full stderr[14:44:49] This is snippy 4.6.0
[14:44:49] Written by Torsten Seemann
[14:44:49] Obtained from https://github.com/tseemann/snippy
[14:44:49] Detected operating system: linux
[14:44:49] Enabling bundled linux tools.
[14:44:49] Found bwa - /usr/local/bin/bwa
[14:44:49] Found bcftools - /usr/local/bin/bcftools
[14:44:49] Found samtools - /usr/local/bin/samtools
[14:44:49] Found java - /usr/local/bin/java
[14:44:49] Found snpEff - /usr/local/bin/snpEff
[14:44:49] Found samclip - /usr/local/bin/samclip
[14:44:49] Found seqtk - /usr/local/bin/seqtk
[14:44:49] Found parallel - /usr/local/bin/parallel
[14:44:49] Found freebayes - /usr/local/bin/freebayes
[14:44:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:44:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:44:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:44:49] Found vcfuniq - /usr/local/bin/vcfuniq
[14:44:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:44:49] Found gzip - /bin/gzip
[14:44:49] Found vt - /usr/local/bin/vt
[14:44:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:44:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:44:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:44:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:44:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:44:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:44:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:44:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 5 | [04:37:03] This is snippy 4.6.0Show full stderr[04:37:03] This is snippy 4.6.0
[04:37:03] Written by Torsten Seemann
[04:37:03] Obtained from https://github.com/tseemann/snippy
[04:37:03] Detected operating system: linux
[04:37:03] Enabling bundled linux tools.
[04:37:03] Found bwa - /usr/local/bin/bwa
[04:37:03] Found bcftools - /usr/local/bin/bcftools
[04:37:03] Found samtools - /usr/local/bin/samtools
[04:37:03] Found java - /usr/local/bin/java
[04:37:03] Found snpEff - /usr/local/bin/snpEff
[04:37:03] Found samclip - /usr/local/bin/samclip
[04:37:03] Found seqtk - /usr/local/bin/seqtk
[04:37:03] Found parallel - /usr/local/bin/parallel
[04:37:03] Found freebayes - /usr/local/bin/freebayes
[04:37:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:03] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:03] Found gzip - /bin/gzip
[04:37:03] Found vt - /usr/local/bin/vt
[04:37:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 5 | [04:43:55] This is snippy 4.6.0Show full stderr[04:43:55] This is snippy 4.6.0
[04:43:55] Written by Torsten Seemann
[04:43:55] Obtained from https://github.com/tseemann/snippy
[04:43:55] Detected operating system: linux
[04:43:55] Enabling bundled linux tools.
[04:43:55] Found bwa - /usr/local/bin/bwa
[04:43:55] Found bcftools - /usr/local/bin/bcftools
[04:43:55] Found samtools - /usr/local/bin/samtools
[04:43:55] Found java - /usr/local/bin/java
[04:43:55] Found snpEff - /usr/local/bin/snpEff
[04:43:55] Found samclip - /usr/local/bin/samclip
[04:43:55] Found seqtk - /usr/local/bin/seqtk
[04:43:55] Found parallel - /usr/local/bin/parallel
[04:43:55] Found freebayes - /usr/local/bin/freebayes
[04:43:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:55] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:56] Found gzip - /bin/gzip
[04:43:56] Found vt - /usr/local/bin/vt
[04:43:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 5 | [07:25:52] This is snippy 4.6.0Show full stderr[07:25:52] This is snippy 4.6.0
[07:25:52] Written by Torsten Seemann
[07:25:52] Obtained from https://github.com/tseemann/snippy
[07:25:52] Detected operating system: linux
[07:25:52] Enabling bundled linux tools.
[07:25:52] Found bwa - /usr/local/bin/bwa
[07:25:52] Found bcftools - /usr/local/bin/bcftools
[07:25:52] Found samtools - /usr/local/bin/samtools
[07:25:52] Found java - /usr/local/bin/java
[07:25:52] Found snpEff - /usr/local/bin/snpEff
[07:25:52] Found samclip - /usr/local/bin/samclip
[07:25:52] Found seqtk - /usr/local/bin/seqtk
[07:25:52] Found parallel - /usr/local/bin/parallel
[07:25:52] Found freebayes - /usr/local/bin/freebayes
[07:25:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:25:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:25:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:25:52] Found vcfuniq - /usr/local/bin/vcfuniq
[07:25:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:25:52] Found gzip - /bin/gzip
[07:25:52] Found vt - /usr/local/bin/vt
[07:25:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:25:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:25:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:25:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:25:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:25:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:25:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:25:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 5 | [07:09:59] This is snippy 4.6.0Show full stderr[07:09:59] This is snippy 4.6.0
[07:09:59] Written by Torsten Seemann
[07:09:59] Obtained from https://github.com/tseemann/snippy
[07:09:59] Detected operating system: linux
[07:09:59] Enabling bundled linux tools.
[07:09:59] Found bwa - /usr/local/bin/bwa
[07:09:59] Found bcftools - /usr/local/bin/bcftools
[07:09:59] Found samtools - /usr/local/bin/samtools
[07:09:59] Found java - /usr/local/bin/java
[07:09:59] Found snpEff - /usr/local/bin/snpEff
[07:09:59] Found samclip - /usr/local/bin/samclip
[07:09:59] Found seqtk - /usr/local/bin/seqtk
[07:09:59] Found parallel - /usr/local/bin/parallel
[07:09:59] Found freebayes - /usr/local/bin/freebayes
[07:09:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:09:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:09:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:09:59] Found vcfuniq - /usr/local/bin/vcfuniq
[07:09:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:09:59] Found gzip - /bin/gzip
[07:09:59] Found vt - /usr/local/bin/vt
[07:09:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:09:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:09:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:09:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:09:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:10:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:10:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:10:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 5 | [07:14:02] This is snippy 4.6.0Show full stderr[07:14:02] This is snippy 4.6.0
[07:14:02] Written by Torsten Seemann
[07:14:02] Obtained from https://github.com/tseemann/snippy
[07:14:02] Detected operating system: linux
[07:14:02] Enabling bundled linux tools.
[07:14:02] Found bwa - /usr/local/bin/bwa
[07:14:02] Found bcftools - /usr/local/bin/bcftools
[07:14:02] Found samtools - /usr/local/bin/samtools
[07:14:02] Found java - /usr/local/bin/java
[07:14:02] Found snpEff - /usr/local/bin/snpEff
[07:14:02] Found samclip - /usr/local/bin/samclip
[07:14:02] Found seqtk - /usr/local/bin/seqtk
[07:14:02] Found parallel - /usr/local/bin/parallel
[07:14:02] Found freebayes - /usr/local/bin/freebayes
[07:14:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:14:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:14:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:14:02] Found vcfuniq - /usr/local/bin/vcfuniq
[07:14:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:14:02] Found gzip - /bin/gzip
[07:14:02] Found vt - /usr/local/bin/vt
[07:14:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:14:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:14:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:14:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:14:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:14:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:14:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:14:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 5 | [09:13:01] This is snippy 4.6.0Show full stderr[09:13:01] This is snippy 4.6.0
[09:13:01] Written by Torsten Seemann
[09:13:01] Obtained from https://github.com/tseemann/snippy
[09:13:01] Detected operating system: linux
[09:13:01] Enabling bundled linux tools.
[09:13:01] Found bwa - /usr/local/bin/bwa
[09:13:01] Found bcftools - /usr/local/bin/bcftools
[09:13:01] Found samtools - /usr/local/bin/samtools
[09:13:01] Found java - /usr/local/bin/java
[09:13:01] Found snpEff - /usr/local/bin/snpEff
[09:13:01] Found samclip - /usr/local/bin/samclip
[09:13:01] Found seqtk - /usr/local/bin/seqtk
[09:13:01] Found parallel - /usr/local/bin/parallel
[09:13:01] Found freebayes - /usr/local/bin/freebayes
[09:13:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:13:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:13:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:13:01] Found vcfuniq - /usr/local/bin/vcfuniq
[09:13:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:13:01] Found gzip - /bin/gzip
[09:13:01] Found vt - /usr/local/bin/vt
[09:13:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:13:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:13:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:13:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:13:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:13:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:13:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:13:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [21:23:37] This is snippy 4.6.0Show full stderr[21:23:37] This is snippy 4.6.0
[21:23:37] Written by Torsten Seemann
[21:23:37] Obtained from https://github.com/tseemann/snippy
[21:23:37] Detected operating system: linux
[21:23:37] Enabling bundled linux tools.
[21:23:37] Found bwa - /usr/local/bin/bwa
[21:23:37] Found bcftools - /usr/local/bin/bcftools
[21:23:37] Found samtools - /usr/local/bin/samtools
[21:23:37] Found java - /usr/local/bin/java
[21:23:37] Found snpEff - /usr/local/bin/snpEff
[21:23:37] Found samclip - /usr/local/bin/samclip
[21:23:37] Found seqtk - /usr/local/bin/seqtk
[21:23:37] Found parallel - /usr/local/bin/parallel
[21:23:37] Found freebayes - /usr/local/bin/freebayes
[21:23:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:23:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:23:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:23:37] Found vcfuniq - /usr/local/bin/vcfuniq
[21:23:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:23:37] Found gzip - /bin/gzip
[21:23:37] Found vt - /usr/local/bin/vt
[21:23:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:23:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:23:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:23:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:23:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:23:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:23:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:23:38] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:23:38] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 4 | [04:36:47] This is snippy 4.6.0Show full stderr[04:36:47] This is snippy 4.6.0
[04:36:47] Written by Torsten Seemann
[04:36:47] Obtained from https://github.com/tseemann/snippy
[04:36:47] Detected operating system: linux
[04:36:47] Enabling bundled linux tools.
[04:36:47] Found bwa - /usr/local/bin/bwa
[04:36:47] Found bcftools - /usr/local/bin/bcftools
[04:36:47] Found samtools - /usr/local/bin/samtools
[04:36:47] Found java - /usr/local/bin/java
[04:36:47] Found snpEff - /usr/local/bin/snpEff
[04:36:47] Found samclip - /usr/local/bin/samclip
[04:36:47] Found seqtk - /usr/local/bin/seqtk
[04:36:47] Found parallel - /usr/local/bin/parallel
[04:36:47] Found freebayes - /usr/local/bin/freebayes
[04:36:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:36:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:36:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:36:47] Found vcfuniq - /usr/local/bin/vcfuniq
[04:36:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:36:47] Found gzip - /bin/gzip
[04:36:47] Found vt - /usr/local/bin/vt
[04:36:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:36:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:36:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:36:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:36:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:36:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:36:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:36:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [04:39:09] This is snippy 4.6.0Show full stderr[04:39:09] This is snippy 4.6.0
[04:39:09] Written by Torsten Seemann
[04:39:09] Obtained from https://github.com/tseemann/snippy
[04:39:09] Detected operating system: linux
[04:39:09] Enabling bundled linux tools.
[04:39:09] Found bwa - /usr/local/bin/bwa
[04:39:09] Found bcftools - /usr/local/bin/bcftools
[04:39:09] Found samtools - /usr/local/bin/samtools
[04:39:09] Found java - /usr/local/bin/java
[04:39:09] Found snpEff - /usr/local/bin/snpEff
[04:39:09] Found samclip - /usr/local/bin/samclip
[04:39:09] Found seqtk - /usr/local/bin/seqtk
[04:39:09] Found parallel - /usr/local/bin/parallel
[04:39:09] Found freebayes - /usr/local/bin/freebayes
[04:39:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:39:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:39:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:39:09] Found vcfuniq - /usr/local/bin/vcfuniq
[04:39:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:39:09] Found gzip - /bin/gzip
[04:39:09] Found vt - /usr/local/bin/vt
[04:39:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:39:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:39:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:39:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:39:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:39:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:39:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:39:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [04:38:18] This is snippy 4.6.0Show full stderr[04:38:18] This is snippy 4.6.0
[04:38:18] Written by Torsten Seemann
[04:38:18] Obtained from https://github.com/tseemann/snippy
[04:38:18] Detected operating system: linux
[04:38:18] Enabling bundled linux tools.
[04:38:18] Found bwa - /usr/local/bin/bwa
[04:38:18] Found bcftools - /usr/local/bin/bcftools
[04:38:18] Found samtools - /usr/local/bin/samtools
[04:38:18] Found java - /usr/local/bin/java
[04:38:18] Found snpEff - /usr/local/bin/snpEff
[04:38:18] Found samclip - /usr/local/bin/samclip
[04:38:18] Found seqtk - /usr/local/bin/seqtk
[04:38:18] Found parallel - /usr/local/bin/parallel
[04:38:18] Found freebayes - /usr/local/bin/freebayes
[04:38:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:18] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:18] Found gzip - /bin/gzip
[04:38:18] Found vt - /usr/local/bin/vt
[04:38:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [04:42:48] This is snippy 4.6.0Show full stderr[04:42:48] This is snippy 4.6.0
[04:42:48] Written by Torsten Seemann
[04:42:48] Obtained from https://github.com/tseemann/snippy
[04:42:48] Detected operating system: linux
[04:42:48] Enabling bundled linux tools.
[04:42:48] Found bwa - /usr/local/bin/bwa
[04:42:48] Found bcftools - /usr/local/bin/bcftools
[04:42:48] Found samtools - /usr/local/bin/samtools
[04:42:48] Found java - /usr/local/bin/java
[04:42:48] Found snpEff - /usr/local/bin/snpEff
[04:42:48] Found samclip - /usr/local/bin/samclip
[04:42:48] Found seqtk - /usr/local/bin/seqtk
[04:42:48] Found parallel - /usr/local/bin/parallel
[04:42:48] Found freebayes - /usr/local/bin/freebayes
[04:42:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:48] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:48] Found gzip - /bin/gzip
[04:42:48] Found vt - /usr/local/bin/vt
[04:42:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [04:54:49] This is snippy 4.6.0Show full stderr[04:54:49] This is snippy 4.6.0
[04:54:49] Written by Torsten Seemann
[04:54:49] Obtained from https://github.com/tseemann/snippy
[04:54:49] Detected operating system: linux
[04:54:49] Enabling bundled linux tools.
[04:54:49] Found bwa - /usr/local/bin/bwa
[04:54:49] Found bcftools - /usr/local/bin/bcftools
[04:54:49] Found samtools - /usr/local/bin/samtools
[04:54:49] Found java - /usr/local/bin/java
[04:54:49] Found snpEff - /usr/local/bin/snpEff
[04:54:49] Found samclip - /usr/local/bin/samclip
[04:54:49] Found seqtk - /usr/local/bin/seqtk
[04:54:49] Found parallel - /usr/local/bin/parallel
[04:54:49] Found freebayes - /usr/local/bin/freebayes
[04:54:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:54:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:54:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:54:49] Found vcfuniq - /usr/local/bin/vcfuniq
[04:54:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:54:49] Found gzip - /bin/gzip
[04:54:49] Found vt - /usr/local/bin/vt
[04:54:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:54:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:54:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:54:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:54:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:54:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:54:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:54:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [04:56:01] This is snippy 4.6.0Show full stderr[04:56:01] This is snippy 4.6.0
[04:56:01] Written by Torsten Seemann
[04:56:01] Obtained from https://github.com/tseemann/snippy
[04:56:01] Detected operating system: linux
[04:56:01] Enabling bundled linux tools.
[04:56:01] Found bwa - /usr/local/bin/bwa
[04:56:01] Found bcftools - /usr/local/bin/bcftools
[04:56:01] Found samtools - /usr/local/bin/samtools
[04:56:01] Found java - /usr/local/bin/java
[04:56:01] Found snpEff - /usr/local/bin/snpEff
[04:56:01] Found samclip - /usr/local/bin/samclip
[04:56:01] Found seqtk - /usr/local/bin/seqtk
[04:56:01] Found parallel - /usr/local/bin/parallel
[04:56:01] Found freebayes - /usr/local/bin/freebayes
[04:56:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:01] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:01] Found gzip - /bin/gzip
[04:56:01] Found vt - /usr/local/bin/vt
[04:56:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [04:56:15] This is snippy 4.6.0Show full stderr[04:56:15] This is snippy 4.6.0
[04:56:15] Written by Torsten Seemann
[04:56:15] Obtained from https://github.com/tseemann/snippy
[04:56:15] Detected operating system: linux
[04:56:15] Enabling bundled linux tools.
[04:56:15] Found bwa - /usr/local/bin/bwa
[04:56:15] Found bcftools - /usr/local/bin/bcftools
[04:56:15] Found samtools - /usr/local/bin/samtools
[04:56:15] Found java - /usr/local/bin/java
[04:56:15] Found snpEff - /usr/local/bin/snpEff
[04:56:15] Found samclip - /usr/local/bin/samclip
[04:56:15] Found seqtk - /usr/local/bin/seqtk
[04:56:15] Found parallel - /usr/local/bin/parallel
[04:56:15] Found freebayes - /usr/local/bin/freebayes
[04:56:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:15] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:15] Found gzip - /bin/gzip
[04:56:15] Found vt - /usr/local/bin/vt
[04:56:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [04:56:30] This is snippy 4.6.0Show full stderr[04:56:30] This is snippy 4.6.0
[04:56:30] Written by Torsten Seemann
[04:56:30] Obtained from https://github.com/tseemann/snippy
[04:56:30] Detected operating system: linux
[04:56:30] Enabling bundled linux tools.
[04:56:30] Found bwa - /usr/local/bin/bwa
[04:56:30] Found bcftools - /usr/local/bin/bcftools
[04:56:30] Found samtools - /usr/local/bin/samtools
[04:56:30] Found java - /usr/local/bin/java
[04:56:30] Found snpEff - /usr/local/bin/snpEff
[04:56:30] Found samclip - /usr/local/bin/samclip
[04:56:30] Found seqtk - /usr/local/bin/seqtk
[04:56:30] Found parallel - /usr/local/bin/parallel
[04:56:30] Found freebayes - /usr/local/bin/freebayes
[04:56:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:30] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:30] Found gzip - /bin/gzip
[04:56:30] Found vt - /usr/local/bin/vt
[04:56:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [04:58:18] This is snippy 4.6.0Show full stderr[04:58:18] This is snippy 4.6.0
[04:58:18] Written by Torsten Seemann
[04:58:18] Obtained from https://github.com/tseemann/snippy
[04:58:18] Detected operating system: linux
[04:58:18] Enabling bundled linux tools.
[04:58:18] Found bwa - /usr/local/bin/bwa
[04:58:18] Found bcftools - /usr/local/bin/bcftools
[04:58:18] Found samtools - /usr/local/bin/samtools
[04:58:18] Found java - /usr/local/bin/java
[04:58:18] Found snpEff - /usr/local/bin/snpEff
[04:58:18] Found samclip - /usr/local/bin/samclip
[04:58:18] Found seqtk - /usr/local/bin/seqtk
[04:58:18] Found parallel - /usr/local/bin/parallel
[04:58:18] Found freebayes - /usr/local/bin/freebayes
[04:58:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:58:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:58:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:58:18] Found vcfuniq - /usr/local/bin/vcfuniq
[04:58:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:58:18] Found gzip - /bin/gzip
[04:58:18] Found vt - /usr/local/bin/vt
[04:58:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:58:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:58:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:58:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:58:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:58:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:58:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:58:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [05:02:20] This is snippy 4.6.0Show full stderr[05:02:20] This is snippy 4.6.0
[05:02:20] Written by Torsten Seemann
[05:02:20] Obtained from https://github.com/tseemann/snippy
[05:02:20] Detected operating system: linux
[05:02:20] Enabling bundled linux tools.
[05:02:20] Found bwa - /usr/local/bin/bwa
[05:02:20] Found bcftools - /usr/local/bin/bcftools
[05:02:20] Found samtools - /usr/local/bin/samtools
[05:02:20] Found java - /usr/local/bin/java
[05:02:20] Found snpEff - /usr/local/bin/snpEff
[05:02:20] Found samclip - /usr/local/bin/samclip
[05:02:20] Found seqtk - /usr/local/bin/seqtk
[05:02:20] Found parallel - /usr/local/bin/parallel
[05:02:20] Found freebayes - /usr/local/bin/freebayes
[05:02:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:20] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:20] Found gzip - /bin/gzip
[05:02:20] Found vt - /usr/local/bin/vt
[05:02:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [05:02:48] This is snippy 4.6.0Show full stderr[05:02:48] This is snippy 4.6.0
[05:02:48] Written by Torsten Seemann
[05:02:48] Obtained from https://github.com/tseemann/snippy
[05:02:48] Detected operating system: linux
[05:02:48] Enabling bundled linux tools.
[05:02:48] Found bwa - /usr/local/bin/bwa
[05:02:48] Found bcftools - /usr/local/bin/bcftools
[05:02:48] Found samtools - /usr/local/bin/samtools
[05:02:48] Found java - /usr/local/bin/java
[05:02:48] Found snpEff - /usr/local/bin/snpEff
[05:02:48] Found samclip - /usr/local/bin/samclip
[05:02:48] Found seqtk - /usr/local/bin/seqtk
[05:02:48] Found parallel - /usr/local/bin/parallel
[05:02:48] Found freebayes - /usr/local/bin/freebayes
[05:02:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:49] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:49] Found gzip - /bin/gzip
[05:02:49] Found vt - /usr/local/bin/vt
[05:02:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [05:05:18] This is snippy 4.6.0Show full stderr[05:05:18] This is snippy 4.6.0
[05:05:18] Written by Torsten Seemann
[05:05:18] Obtained from https://github.com/tseemann/snippy
[05:05:18] Detected operating system: linux
[05:05:18] Enabling bundled linux tools.
[05:05:18] Found bwa - /usr/local/bin/bwa
[05:05:18] Found bcftools - /usr/local/bin/bcftools
[05:05:18] Found samtools - /usr/local/bin/samtools
[05:05:18] Found java - /usr/local/bin/java
[05:05:18] Found snpEff - /usr/local/bin/snpEff
[05:05:18] Found samclip - /usr/local/bin/samclip
[05:05:18] Found seqtk - /usr/local/bin/seqtk
[05:05:18] Found parallel - /usr/local/bin/parallel
[05:05:18] Found freebayes - /usr/local/bin/freebayes
[05:05:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:18] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:18] Found gzip - /bin/gzip
[05:05:18] Found vt - /usr/local/bin/vt
[05:05:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [05:06:21] This is snippy 4.6.0Show full stderr[05:06:21] This is snippy 4.6.0
[05:06:21] Written by Torsten Seemann
[05:06:21] Obtained from https://github.com/tseemann/snippy
[05:06:21] Detected operating system: linux
[05:06:21] Enabling bundled linux tools.
[05:06:21] Found bwa - /usr/local/bin/bwa
[05:06:21] Found bcftools - /usr/local/bin/bcftools
[05:06:21] Found samtools - /usr/local/bin/samtools
[05:06:21] Found java - /usr/local/bin/java
[05:06:21] Found snpEff - /usr/local/bin/snpEff
[05:06:21] Found samclip - /usr/local/bin/samclip
[05:06:21] Found seqtk - /usr/local/bin/seqtk
[05:06:21] Found parallel - /usr/local/bin/parallel
[05:06:21] Found freebayes - /usr/local/bin/freebayes
[05:06:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:06:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:06:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:06:21] Found vcfuniq - /usr/local/bin/vcfuniq
[05:06:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:06:21] Found gzip - /bin/gzip
[05:06:21] Found vt - /usr/local/bin/vt
[05:06:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:06:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:06:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:06:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:06:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:06:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:06:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:06:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [05:06:36] This is snippy 4.6.0Show full stderr[05:06:36] This is snippy 4.6.0
[05:06:36] Written by Torsten Seemann
[05:06:36] Obtained from https://github.com/tseemann/snippy
[05:06:36] Detected operating system: linux
[05:06:36] Enabling bundled linux tools.
[05:06:36] Found bwa - /usr/local/bin/bwa
[05:06:36] Found bcftools - /usr/local/bin/bcftools
[05:06:36] Found samtools - /usr/local/bin/samtools
[05:06:36] Found java - /usr/local/bin/java
[05:06:36] Found snpEff - /usr/local/bin/snpEff
[05:06:36] Found samclip - /usr/local/bin/samclip
[05:06:36] Found seqtk - /usr/local/bin/seqtk
[05:06:36] Found parallel - /usr/local/bin/parallel
[05:06:36] Found freebayes - /usr/local/bin/freebayes
[05:06:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:06:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:06:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:06:36] Found vcfuniq - /usr/local/bin/vcfuniq
[05:06:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:06:36] Found gzip - /bin/gzip
[05:06:36] Found vt - /usr/local/bin/vt
[05:06:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:06:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:06:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:06:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:06:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:06:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:06:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:06:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [05:06:52] This is snippy 4.6.0Show full stderr[05:06:52] This is snippy 4.6.0
[05:06:52] Written by Torsten Seemann
[05:06:52] Obtained from https://github.com/tseemann/snippy
[05:06:52] Detected operating system: linux
[05:06:52] Enabling bundled linux tools.
[05:06:52] Found bwa - /usr/local/bin/bwa
[05:06:52] Found bcftools - /usr/local/bin/bcftools
[05:06:52] Found samtools - /usr/local/bin/samtools
[05:06:52] Found java - /usr/local/bin/java
[05:06:52] Found snpEff - /usr/local/bin/snpEff
[05:06:52] Found samclip - /usr/local/bin/samclip
[05:06:52] Found seqtk - /usr/local/bin/seqtk
[05:06:52] Found parallel - /usr/local/bin/parallel
[05:06:52] Found freebayes - /usr/local/bin/freebayes
[05:06:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:06:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:06:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:06:52] Found vcfuniq - /usr/local/bin/vcfuniq
[05:06:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:06:52] Found gzip - /bin/gzip
[05:06:52] Found vt - /usr/local/bin/vt
[05:06:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:06:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:06:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:06:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:06:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:06:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:06:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:06:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [03:39:40] This is snippy 4.6.0Show full stderr[03:39:40] This is snippy 4.6.0
[03:39:40] Written by Torsten Seemann
[03:39:40] Obtained from https://github.com/tseemann/snippy
[03:39:40] Detected operating system: linux
[03:39:40] Enabling bundled linux tools.
[03:39:40] Found bwa - /usr/local/bin/bwa
[03:39:40] Found bcftools - /usr/local/bin/bcftools
[03:39:40] Found samtools - /usr/local/bin/samtools
[03:39:40] Found java - /usr/local/bin/java
[03:39:40] Found snpEff - /usr/local/bin/snpEff
[03:39:40] Found samclip - /usr/local/bin/samclip
[03:39:40] Found seqtk - /usr/local/bin/seqtk
[03:39:40] Found parallel - /usr/local/bin/parallel
[03:39:40] Found freebayes - /usr/local/bin/freebayes
[03:39:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:39:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:39:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:39:40] Found vcfuniq - /usr/local/bin/vcfuniq
[03:39:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:39:40] Found gzip - /bin/gzip
[03:39:40] Found vt - /usr/local/bin/vt
[03:39:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:39:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:39:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:39:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:39:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:39:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:39:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:39:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [03:39:56] This is snippy 4.6.0Show full stderr[03:39:56] This is snippy 4.6.0
[03:39:56] Written by Torsten Seemann
[03:39:56] Obtained from https://github.com/tseemann/snippy
[03:39:56] Detected operating system: linux
[03:39:56] Enabling bundled linux tools.
[03:39:56] Found bwa - /usr/local/bin/bwa
[03:39:56] Found bcftools - /usr/local/bin/bcftools
[03:39:56] Found samtools - /usr/local/bin/samtools
[03:39:56] Found java - /usr/local/bin/java
[03:39:56] Found snpEff - /usr/local/bin/snpEff
[03:39:56] Found samclip - /usr/local/bin/samclip
[03:39:56] Found seqtk - /usr/local/bin/seqtk
[03:39:56] Found parallel - /usr/local/bin/parallel
[03:39:56] Found freebayes - /usr/local/bin/freebayes
[03:39:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:39:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:39:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:39:56] Found vcfuniq - /usr/local/bin/vcfuniq
[03:39:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:39:56] Found gzip - /bin/gzip
[03:39:56] Found vt - /usr/local/bin/vt
[03:39:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:39:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:39:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:39:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:39:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:39:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:39:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:39:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [03:41:42] This is snippy 4.6.0Show full stderr[03:41:42] This is snippy 4.6.0
[03:41:42] Written by Torsten Seemann
[03:41:42] Obtained from https://github.com/tseemann/snippy
[03:41:42] Detected operating system: linux
[03:41:42] Enabling bundled linux tools.
[03:41:42] Found bwa - /usr/local/bin/bwa
[03:41:42] Found bcftools - /usr/local/bin/bcftools
[03:41:42] Found samtools - /usr/local/bin/samtools
[03:41:42] Found java - /usr/local/bin/java
[03:41:42] Found snpEff - /usr/local/bin/snpEff
[03:41:42] Found samclip - /usr/local/bin/samclip
[03:41:42] Found seqtk - /usr/local/bin/seqtk
[03:41:42] Found parallel - /usr/local/bin/parallel
[03:41:42] Found freebayes - /usr/local/bin/freebayes
[03:41:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:41:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:41:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:41:42] Found vcfuniq - /usr/local/bin/vcfuniq
[03:41:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:41:42] Found gzip - /bin/gzip
[03:41:42] Found vt - /usr/local/bin/vt
[03:41:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:41:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:41:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:41:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:41:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:41:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:41:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:41:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [03:41:57] This is snippy 4.6.0Show full stderr[03:41:57] This is snippy 4.6.0
[03:41:57] Written by Torsten Seemann
[03:41:57] Obtained from https://github.com/tseemann/snippy
[03:41:57] Detected operating system: linux
[03:41:57] Enabling bundled linux tools.
[03:41:57] Found bwa - /usr/local/bin/bwa
[03:41:57] Found bcftools - /usr/local/bin/bcftools
[03:41:57] Found samtools - /usr/local/bin/samtools
[03:41:57] Found java - /usr/local/bin/java
[03:41:57] Found snpEff - /usr/local/bin/snpEff
[03:41:57] Found samclip - /usr/local/bin/samclip
[03:41:57] Found seqtk - /usr/local/bin/seqtk
[03:41:57] Found parallel - /usr/local/bin/parallel
[03:41:57] Found freebayes - /usr/local/bin/freebayes
[03:41:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:41:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:41:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:41:57] Found vcfuniq - /usr/local/bin/vcfuniq
[03:41:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:41:57] Found gzip - /bin/gzip
[03:41:57] Found vt - /usr/local/bin/vt
[03:41:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:41:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:41:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:41:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:41:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:41:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:41:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:41:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [03:42:35] This is snippy 4.6.0Show full stderr[03:42:35] This is snippy 4.6.0
[03:42:35] Written by Torsten Seemann
[03:42:35] Obtained from https://github.com/tseemann/snippy
[03:42:35] Detected operating system: linux
[03:42:35] Enabling bundled linux tools.
[03:42:35] Found bwa - /usr/local/bin/bwa
[03:42:35] Found bcftools - /usr/local/bin/bcftools
[03:42:35] Found samtools - /usr/local/bin/samtools
[03:42:35] Found java - /usr/local/bin/java
[03:42:35] Found snpEff - /usr/local/bin/snpEff
[03:42:35] Found samclip - /usr/local/bin/samclip
[03:42:35] Found seqtk - /usr/local/bin/seqtk
[03:42:35] Found parallel - /usr/local/bin/parallel
[03:42:35] Found freebayes - /usr/local/bin/freebayes
[03:42:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:35] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:35] Found gzip - /bin/gzip
[03:42:35] Found vt - /usr/local/bin/vt
[03:42:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [03:42:53] This is snippy 4.6.0Show full stderr[03:42:53] This is snippy 4.6.0
[03:42:53] Written by Torsten Seemann
[03:42:53] Obtained from https://github.com/tseemann/snippy
[03:42:53] Detected operating system: linux
[03:42:53] Enabling bundled linux tools.
[03:42:53] Found bwa - /usr/local/bin/bwa
[03:42:53] Found bcftools - /usr/local/bin/bcftools
[03:42:53] Found samtools - /usr/local/bin/samtools
[03:42:53] Found java - /usr/local/bin/java
[03:42:53] Found snpEff - /usr/local/bin/snpEff
[03:42:53] Found samclip - /usr/local/bin/samclip
[03:42:53] Found seqtk - /usr/local/bin/seqtk
[03:42:53] Found parallel - /usr/local/bin/parallel
[03:42:53] Found freebayes - /usr/local/bin/freebayes
[03:42:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:53] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:53] Found gzip - /bin/gzip
[03:42:53] Found vt - /usr/local/bin/vt
[03:42:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [05:58:56] This is snippy 4.6.0Show full stderr[05:58:56] This is snippy 4.6.0
[05:58:56] Written by Torsten Seemann
[05:58:56] Obtained from https://github.com/tseemann/snippy
[05:58:56] Detected operating system: linux
[05:58:56] Enabling bundled linux tools.
[05:58:56] Found bwa - /usr/local/bin/bwa
[05:58:56] Found bcftools - /usr/local/bin/bcftools
[05:58:56] Found samtools - /usr/local/bin/samtools
[05:58:56] Found java - /usr/local/bin/java
[05:58:56] Found snpEff - /usr/local/bin/snpEff
[05:58:56] Found samclip - /usr/local/bin/samclip
[05:58:56] Found seqtk - /usr/local/bin/seqtk
[05:58:56] Found parallel - /usr/local/bin/parallel
[05:58:56] Found freebayes - /usr/local/bin/freebayes
[05:58:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:58:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:58:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:58:56] Found vcfuniq - /usr/local/bin/vcfuniq
[05:58:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:58:56] Found gzip - /bin/gzip
[05:58:56] Found vt - /usr/local/bin/vt
[05:58:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:58:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:58:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:58:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:58:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:58:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:58:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:58:57] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:58:57] Treating reference as 'fasta' format.
[05:58:57] Will use 1 CPU cores.
[05:58:57] Using read file: /corral4/main/objects/9/5/0/dataset_950f8e91-ffa2-498f-b788-3bc522be3ba4.dat
[05:58:57] Creating folder: Resistance_70_fasta
[05:58:57] Changing working directory: Resistance_70_fasta
[05:58:57] Creating reference folder: reference
[05:58:57] Extracting FASTA and GFF from reference.
[05:58:57] Wrote 3 sequences to ref.fa
[05:58:57] Wrote 0 features to ref.gff
[05:58:57] Shredding /corral4/main/objects/9/5/0/dataset_950f8e91-ffa2-498f-b788-3bc522be3ba4.dat into pseudo-reads
[05:59:02] Wrote 396876 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:59:02] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[05:59:02] Using BAM RG (Read Group) ID: Resistance_70_fasta
[05:59:02] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:59:02] Error running command, check Resistance_70_fasta/snps.log |
| 4 | [05:58:31] This is snippy 4.6.0Show full stderr[05:58:31] This is snippy 4.6.0
[05:58:31] Written by Torsten Seemann
[05:58:31] Obtained from https://github.com/tseemann/snippy
[05:58:31] Detected operating system: linux
[05:58:31] Enabling bundled linux tools.
[05:58:31] Found bwa - /usr/local/bin/bwa
[05:58:31] Found bcftools - /usr/local/bin/bcftools
[05:58:31] Found samtools - /usr/local/bin/samtools
[05:58:31] Found java - /usr/local/bin/java
[05:58:31] Found snpEff - /usr/local/bin/snpEff
[05:58:31] Found samclip - /usr/local/bin/samclip
[05:58:31] Found seqtk - /usr/local/bin/seqtk
[05:58:31] Found parallel - /usr/local/bin/parallel
[05:58:31] Found freebayes - /usr/local/bin/freebayes
[05:58:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:58:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:58:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:58:31] Found vcfuniq - /usr/local/bin/vcfuniq
[05:58:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:58:31] Found gzip - /bin/gzip
[05:58:31] Found vt - /usr/local/bin/vt
[05:58:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:58:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:58:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:58:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:58:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:58:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:58:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:58:32] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:58:32] Treating reference as 'fasta' format.
[05:58:32] Will use 1 CPU cores.
[05:58:32] Using read file: /corral4/main/objects/4/7/b/dataset_47b089a5-7ccc-49f2-b505-f2adb97b524c.dat
[05:58:32] Creating folder: Resistance_93_fasta
[05:58:32] Changing working directory: Resistance_93_fasta
[05:58:32] Creating reference folder: reference
[05:58:32] Extracting FASTA and GFF from reference.
[05:58:32] Wrote 3 sequences to ref.fa
[05:58:32] Wrote 0 features to ref.gff
[05:58:32] Shredding /corral4/main/objects/4/7/b/dataset_47b089a5-7ccc-49f2-b505-f2adb97b524c.dat into pseudo-reads
[05:58:37] Wrote 422488 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:58:37] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:58:37] Using BAM RG (Read Group) ID: Resistance_93_fasta
[05:58:38] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:58:38] Running: bwa index reference/ref.fa 2>> snps.log
[05:58:41] Error running command, check Resistance_93_fasta/snps.log |
| 4 | [07:05:57] This is snippy 4.6.0Show full stderr[07:05:57] This is snippy 4.6.0
[07:05:57] Written by Torsten Seemann
[07:05:57] Obtained from https://github.com/tseemann/snippy
[07:05:57] Detected operating system: linux
[07:05:57] Enabling bundled linux tools.
[07:05:57] Found bwa - /usr/local/bin/bwa
[07:05:57] Found bcftools - /usr/local/bin/bcftools
[07:05:57] Found samtools - /usr/local/bin/samtools
[07:05:57] Found java - /usr/local/bin/java
[07:05:57] Found snpEff - /usr/local/bin/snpEff
[07:05:57] Found samclip - /usr/local/bin/samclip
[07:05:57] Found seqtk - /usr/local/bin/seqtk
[07:05:57] Found parallel - /usr/local/bin/parallel
[07:05:57] Found freebayes - /usr/local/bin/freebayes
[07:05:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:57] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:57] Found gzip - /bin/gzip
[07:05:57] Found vt - /usr/local/bin/vt
[07:05:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:58] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:05:58] Treating reference as 'fasta' format.
[07:05:58] Will use 1 CPU cores.
[07:05:58] Using read file: /corral4/main/objects/f/9/1/dataset_f91c1dae-8edf-47ef-85e8-e7216580cbc0.dat
[07:05:58] Creating folder: BVBRC_genome_sequence___2025_10_25T135718_903_fasta
[07:05:58] Changing working directory: BVBRC_genome_sequence___2025_10_25T135718_903_fasta
[07:05:58] Creating reference folder: reference
[07:05:58] Extracting FASTA and GFF from reference.
[07:05:58] Wrote 1 sequences to ref.fa
[07:05:58] Wrote 0 features to ref.gff
[07:05:58] Shredding /corral4/main/objects/f/9/1/dataset_f91c1dae-8edf-47ef-85e8-e7216580cbc0.dat into pseudo-reads
[07:06:00] Wrote 221700 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:06:00] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[07:06:00] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135718_903_fasta
[07:06:00] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:06:00] Running: bwa index reference/ref.fa 2>> snps.log
[07:06:01] Error running command, check BVBRC_genome_sequence___2025_10_25T135718_903_fasta/snps.log |
| 4 | [06:48:03] This is snippy 4.6.0Show full stderr[06:48:03] This is snippy 4.6.0
[06:48:03] Written by Torsten Seemann
[06:48:03] Obtained from https://github.com/tseemann/snippy
[06:48:03] Detected operating system: linux
[06:48:03] Enabling bundled linux tools.
[06:48:03] Found bwa - /usr/local/bin/bwa
[06:48:03] Found bcftools - /usr/local/bin/bcftools
[06:48:03] Found samtools - /usr/local/bin/samtools
[06:48:03] Found java - /usr/local/bin/java
[06:48:03] Found snpEff - /usr/local/bin/snpEff
[06:48:03] Found samclip - /usr/local/bin/samclip
[06:48:03] Found seqtk - /usr/local/bin/seqtk
[06:48:03] Found parallel - /usr/local/bin/parallel
[06:48:03] Found freebayes - /usr/local/bin/freebayes
[06:48:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:03] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:03] Found gzip - /bin/gzip
[06:48:03] Found vt - /usr/local/bin/vt
[06:48:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [07:12:32] This is snippy 4.6.0Show full stderr[07:12:32] This is snippy 4.6.0
[07:12:32] Written by Torsten Seemann
[07:12:32] Obtained from https://github.com/tseemann/snippy
[07:12:32] Detected operating system: linux
[07:12:32] Enabling bundled linux tools.
[07:12:32] Found bwa - /usr/local/bin/bwa
[07:12:32] Found bcftools - /usr/local/bin/bcftools
[07:12:32] Found samtools - /usr/local/bin/samtools
[07:12:32] Found java - /usr/local/bin/java
[07:12:32] Found snpEff - /usr/local/bin/snpEff
[07:12:32] Found samclip - /usr/local/bin/samclip
[07:12:32] Found seqtk - /usr/local/bin/seqtk
[07:12:32] Found parallel - /usr/local/bin/parallel
[07:12:32] Found freebayes - /usr/local/bin/freebayes
[07:12:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:12:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:12:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:12:32] Found vcfuniq - /usr/local/bin/vcfuniq
[07:12:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:12:32] Found gzip - /bin/gzip
[07:12:32] Found vt - /usr/local/bin/vt
[07:12:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:12:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:12:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:12:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:12:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:12:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:12:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:12:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [06:57:22] This is snippy 4.6.0Show full stderr[06:57:22] This is snippy 4.6.0
[06:57:22] Written by Torsten Seemann
[06:57:22] Obtained from https://github.com/tseemann/snippy
[06:57:22] Detected operating system: linux
[06:57:22] Enabling bundled linux tools.
[06:57:22] Found bwa - /usr/local/bin/bwa
[06:57:22] Found bcftools - /usr/local/bin/bcftools
[06:57:22] Found samtools - /usr/local/bin/samtools
[06:57:22] Found java - /usr/local/bin/java
[06:57:22] Found snpEff - /usr/local/bin/snpEff
[06:57:22] Found samclip - /usr/local/bin/samclip
[06:57:22] Found seqtk - /usr/local/bin/seqtk
[06:57:22] Found parallel - /usr/local/bin/parallel
[06:57:22] Found freebayes - /usr/local/bin/freebayes
[06:57:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:57:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:57:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:57:22] Found vcfuniq - /usr/local/bin/vcfuniq
[06:57:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:57:22] Found gzip - /bin/gzip
[06:57:22] Found vt - /usr/local/bin/vt
[06:57:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:57:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:57:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:57:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:57:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:57:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:57:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:57:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [07:01:10] This is snippy 4.6.0Show full stderr[07:01:10] This is snippy 4.6.0
[07:01:10] Written by Torsten Seemann
[07:01:10] Obtained from https://github.com/tseemann/snippy
[07:01:10] Detected operating system: linux
[07:01:10] Enabling bundled linux tools.
[07:01:10] Found bwa - /usr/local/bin/bwa
[07:01:10] Found bcftools - /usr/local/bin/bcftools
[07:01:10] Found samtools - /usr/local/bin/samtools
[07:01:10] Found java - /usr/local/bin/java
[07:01:10] Found snpEff - /usr/local/bin/snpEff
[07:01:10] Found samclip - /usr/local/bin/samclip
[07:01:10] Found seqtk - /usr/local/bin/seqtk
[07:01:10] Found parallel - /usr/local/bin/parallel
[07:01:10] Found freebayes - /usr/local/bin/freebayes
[07:01:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:01:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:01:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:01:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:01:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:01:10] Found gzip - /bin/gzip
[07:01:10] Found vt - /usr/local/bin/vt
[07:01:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:01:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:01:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:01:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:01:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:01:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:01:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:01:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [07:01:24] This is snippy 4.6.0Show full stderr[07:01:24] This is snippy 4.6.0
[07:01:24] Written by Torsten Seemann
[07:01:24] Obtained from https://github.com/tseemann/snippy
[07:01:24] Detected operating system: linux
[07:01:24] Enabling bundled linux tools.
[07:01:24] Found bwa - /usr/local/bin/bwa
[07:01:24] Found bcftools - /usr/local/bin/bcftools
[07:01:24] Found samtools - /usr/local/bin/samtools
[07:01:24] Found java - /usr/local/bin/java
[07:01:24] Found snpEff - /usr/local/bin/snpEff
[07:01:24] Found samclip - /usr/local/bin/samclip
[07:01:24] Found seqtk - /usr/local/bin/seqtk
[07:01:24] Found parallel - /usr/local/bin/parallel
[07:01:24] Found freebayes - /usr/local/bin/freebayes
[07:01:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:01:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:01:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:01:24] Found vcfuniq - /usr/local/bin/vcfuniq
[07:01:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:01:24] Found gzip - /bin/gzip
[07:01:24] Found vt - /usr/local/bin/vt
[07:01:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:01:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:01:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:01:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:01:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:01:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:01:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:01:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [07:00:55] This is snippy 4.6.0Show full stderr[07:00:55] This is snippy 4.6.0
[07:00:55] Written by Torsten Seemann
[07:00:55] Obtained from https://github.com/tseemann/snippy
[07:00:55] Detected operating system: linux
[07:00:55] Enabling bundled linux tools.
[07:00:55] Found bwa - /usr/local/bin/bwa
[07:00:55] Found bcftools - /usr/local/bin/bcftools
[07:00:55] Found samtools - /usr/local/bin/samtools
[07:00:55] Found java - /usr/local/bin/java
[07:00:55] Found snpEff - /usr/local/bin/snpEff
[07:00:55] Found samclip - /usr/local/bin/samclip
[07:00:55] Found seqtk - /usr/local/bin/seqtk
[07:00:55] Found parallel - /usr/local/bin/parallel
[07:00:55] Found freebayes - /usr/local/bin/freebayes
[07:00:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:55] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:55] Found gzip - /bin/gzip
[07:00:55] Found vt - /usr/local/bin/vt
[07:00:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [07:13:30] This is snippy 4.6.0Show full stderr[07:13:30] This is snippy 4.6.0
[07:13:30] Written by Torsten Seemann
[07:13:30] Obtained from https://github.com/tseemann/snippy
[07:13:30] Detected operating system: linux
[07:13:30] Enabling bundled linux tools.
[07:13:30] Found bwa - /usr/local/bin/bwa
[07:13:30] Found bcftools - /usr/local/bin/bcftools
[07:13:30] Found samtools - /usr/local/bin/samtools
[07:13:30] Found java - /usr/local/bin/java
[07:13:30] Found snpEff - /usr/local/bin/snpEff
[07:13:30] Found samclip - /usr/local/bin/samclip
[07:13:30] Found seqtk - /usr/local/bin/seqtk
[07:13:30] Found parallel - /usr/local/bin/parallel
[07:13:30] Found freebayes - /usr/local/bin/freebayes
[07:13:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:13:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:13:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:13:30] Found vcfuniq - /usr/local/bin/vcfuniq
[07:13:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:13:30] Found gzip - /bin/gzip
[07:13:31] Found vt - /usr/local/bin/vt
[07:13:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:13:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:13:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:13:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:13:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:13:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:13:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:13:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [07:10:13] This is snippy 4.6.0Show full stderr[07:10:13] This is snippy 4.6.0
[07:10:13] Written by Torsten Seemann
[07:10:13] Obtained from https://github.com/tseemann/snippy
[07:10:13] Detected operating system: linux
[07:10:13] Enabling bundled linux tools.
[07:10:13] Found bwa - /usr/local/bin/bwa
[07:10:13] Found bcftools - /usr/local/bin/bcftools
[07:10:13] Found samtools - /usr/local/bin/samtools
[07:10:13] Found java - /usr/local/bin/java
[07:10:13] Found snpEff - /usr/local/bin/snpEff
[07:10:13] Found samclip - /usr/local/bin/samclip
[07:10:13] Found seqtk - /usr/local/bin/seqtk
[07:10:13] Found parallel - /usr/local/bin/parallel
[07:10:13] Found freebayes - /usr/local/bin/freebayes
[07:10:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:10:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:10:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:10:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:10:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:10:13] Found gzip - /bin/gzip
[07:10:13] Found vt - /usr/local/bin/vt
[07:10:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:10:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:10:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:10:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:10:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:10:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:10:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:10:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [07:10:42] This is snippy 4.6.0Show full stderr[07:10:42] This is snippy 4.6.0
[07:10:42] Written by Torsten Seemann
[07:10:42] Obtained from https://github.com/tseemann/snippy
[07:10:42] Detected operating system: linux
[07:10:42] Enabling bundled linux tools.
[07:10:42] Found bwa - /usr/local/bin/bwa
[07:10:42] Found bcftools - /usr/local/bin/bcftools
[07:10:42] Found samtools - /usr/local/bin/samtools
[07:10:42] Found java - /usr/local/bin/java
[07:10:42] Found snpEff - /usr/local/bin/snpEff
[07:10:42] Found samclip - /usr/local/bin/samclip
[07:10:42] Found seqtk - /usr/local/bin/seqtk
[07:10:42] Found parallel - /usr/local/bin/parallel
[07:10:42] Found freebayes - /usr/local/bin/freebayes
[07:10:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:10:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:10:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:10:42] Found vcfuniq - /usr/local/bin/vcfuniq
[07:10:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:10:42] Found gzip - /bin/gzip
[07:10:42] Found vt - /usr/local/bin/vt
[07:10:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:10:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:10:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:10:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:10:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:10:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:10:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:10:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [07:14:41] This is snippy 4.6.0Show full stderr[07:14:41] This is snippy 4.6.0
[07:14:41] Written by Torsten Seemann
[07:14:41] Obtained from https://github.com/tseemann/snippy
[07:14:41] Detected operating system: linux
[07:14:41] Enabling bundled linux tools.
[07:14:41] Found bwa - /usr/local/bin/bwa
[07:14:41] Found bcftools - /usr/local/bin/bcftools
[07:14:41] Found samtools - /usr/local/bin/samtools
[07:14:41] Found java - /usr/local/bin/java
[07:14:41] Found snpEff - /usr/local/bin/snpEff
[07:14:41] Found samclip - /usr/local/bin/samclip
[07:14:41] Found seqtk - /usr/local/bin/seqtk
[07:14:41] Found parallel - /usr/local/bin/parallel
[07:14:41] Found freebayes - /usr/local/bin/freebayes
[07:14:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:14:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:14:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:14:41] Found vcfuniq - /usr/local/bin/vcfuniq
[07:14:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:14:41] Found gzip - /bin/gzip
[07:14:41] Found vt - /usr/local/bin/vt
[07:14:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:14:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:14:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:14:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:14:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:14:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:14:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:14:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [07:14:14] This is snippy 4.6.0Show full stderr[07:14:14] This is snippy 4.6.0
[07:14:14] Written by Torsten Seemann
[07:14:14] Obtained from https://github.com/tseemann/snippy
[07:14:14] Detected operating system: linux
[07:14:14] Enabling bundled linux tools.
[07:14:14] Found bwa - /usr/local/bin/bwa
[07:14:14] Found bcftools - /usr/local/bin/bcftools
[07:14:14] Found samtools - /usr/local/bin/samtools
[07:14:14] Found java - /usr/local/bin/java
[07:14:14] Found snpEff - /usr/local/bin/snpEff
[07:14:14] Found samclip - /usr/local/bin/samclip
[07:14:14] Found seqtk - /usr/local/bin/seqtk
[07:14:14] Found parallel - /usr/local/bin/parallel
[07:14:14] Found freebayes - /usr/local/bin/freebayes
[07:14:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:14:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:14:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:14:14] Found vcfuniq - /usr/local/bin/vcfuniq
[07:14:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:14:14] Found gzip - /bin/gzip
[07:14:14] Found vt - /usr/local/bin/vt
[07:14:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:14:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:14:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:14:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:14:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:14:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:14:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:14:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [07:25:35] This is snippy 4.6.0Show full stderr[07:25:35] This is snippy 4.6.0
[07:25:35] Written by Torsten Seemann
[07:25:35] Obtained from https://github.com/tseemann/snippy
[07:25:35] Detected operating system: linux
[07:25:35] Enabling bundled linux tools.
[07:25:35] Found bwa - /usr/local/bin/bwa
[07:25:35] Found bcftools - /usr/local/bin/bcftools
[07:25:35] Found samtools - /usr/local/bin/samtools
[07:25:35] Found java - /usr/local/bin/java
[07:25:35] Found snpEff - /usr/local/bin/snpEff
[07:25:35] Found samclip - /usr/local/bin/samclip
[07:25:35] Found seqtk - /usr/local/bin/seqtk
[07:25:35] Found parallel - /usr/local/bin/parallel
[07:25:35] Found freebayes - /usr/local/bin/freebayes
[07:25:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:25:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:25:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:25:35] Found vcfuniq - /usr/local/bin/vcfuniq
[07:25:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:25:35] Found gzip - /bin/gzip
[07:25:35] Found vt - /usr/local/bin/vt
[07:25:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:25:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:25:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:25:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:25:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:25:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:25:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:25:36] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:25:36] Treating reference as 'fasta' format.
[07:25:36] Will use 1 CPU cores.
[07:25:36] Using read file: /corral4/main/objects/0/e/9/dataset_0e967aab-1d11-4057-ab74-1b27a9a4c8ef.dat
[07:25:36] Creating folder: BVBRC_genome_sequence__78__fasta
[07:25:36] Changing working directory: BVBRC_genome_sequence__78__fasta
[07:25:36] Creating reference folder: reference
[07:25:36] Extracting FASTA and GFF from reference.
[07:25:36] Wrote 1 sequences to ref.fa
[07:25:36] Wrote 0 features to ref.gff
[07:25:36] Shredding /corral4/main/objects/0/e/9/dataset_0e967aab-1d11-4057-ab74-1b27a9a4c8ef.dat into pseudo-reads
[07:25:39] Wrote 216932 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:25:39] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[07:25:39] Using BAM RG (Read Group) ID: BVBRC_genome_sequence__78__fasta
[07:25:39] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:25:39] Running: bwa index reference/ref.fa 2>> snps.log
[07:25:40] Error running command, check BVBRC_genome_sequence__78__fasta/snps.log |
| 4 | [07:28:00] This is snippy 4.6.0Show full stderr[07:28:00] This is snippy 4.6.0
[07:28:00] Written by Torsten Seemann
[07:28:00] Obtained from https://github.com/tseemann/snippy
[07:28:00] Detected operating system: linux
[07:28:00] Enabling bundled linux tools.
[07:28:00] Found bwa - /usr/local/bin/bwa
[07:28:00] Found bcftools - /usr/local/bin/bcftools
[07:28:00] Found samtools - /usr/local/bin/samtools
[07:28:00] Found java - /usr/local/bin/java
[07:28:01] Found snpEff - /usr/local/bin/snpEff
[07:28:01] Found samclip - /usr/local/bin/samclip
[07:28:01] Found seqtk - /usr/local/bin/seqtk
[07:28:01] Found parallel - /usr/local/bin/parallel
[07:28:01] Found freebayes - /usr/local/bin/freebayes
[07:28:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:28:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:28:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:28:01] Found vcfuniq - /usr/local/bin/vcfuniq
[07:28:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:28:01] Found gzip - /bin/gzip
[07:28:01] Found vt - /usr/local/bin/vt
[07:28:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:28:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:28:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:28:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:28:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:28:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:28:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:28:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [07:33:32] This is snippy 4.6.0Show full stderr[07:33:32] This is snippy 4.6.0
[07:33:32] Written by Torsten Seemann
[07:33:32] Obtained from https://github.com/tseemann/snippy
[07:33:32] Detected operating system: linux
[07:33:32] Enabling bundled linux tools.
[07:33:32] Found bwa - /usr/local/bin/bwa
[07:33:32] Found bcftools - /usr/local/bin/bcftools
[07:33:32] Found samtools - /usr/local/bin/samtools
[07:33:32] Found java - /usr/local/bin/java
[07:33:32] Found snpEff - /usr/local/bin/snpEff
[07:33:32] Found samclip - /usr/local/bin/samclip
[07:33:32] Found seqtk - /usr/local/bin/seqtk
[07:33:32] Found parallel - /usr/local/bin/parallel
[07:33:32] Found freebayes - /usr/local/bin/freebayes
[07:33:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:33:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:33:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:33:32] Found vcfuniq - /usr/local/bin/vcfuniq
[07:33:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:33:32] Found gzip - /bin/gzip
[07:33:32] Found vt - /usr/local/bin/vt
[07:33:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:33:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:33:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:33:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:33:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:33:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:33:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:33:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [09:21:19] This is snippy 4.6.0Show full stderr[09:21:19] This is snippy 4.6.0
[09:21:19] Written by Torsten Seemann
[09:21:19] Obtained from https://github.com/tseemann/snippy
[09:21:19] Detected operating system: linux
[09:21:19] Enabling bundled linux tools.
[09:21:19] Found bwa - /usr/local/bin/bwa
[09:21:19] Found bcftools - /usr/local/bin/bcftools
[09:21:19] Found samtools - /usr/local/bin/samtools
[09:21:19] Found java - /usr/local/bin/java
[09:21:19] Found snpEff - /usr/local/bin/snpEff
[09:21:19] Found samclip - /usr/local/bin/samclip
[09:21:19] Found seqtk - /usr/local/bin/seqtk
[09:21:19] Found parallel - /usr/local/bin/parallel
[09:21:19] Found freebayes - /usr/local/bin/freebayes
[09:21:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:21:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:21:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:21:19] Found vcfuniq - /usr/local/bin/vcfuniq
[09:21:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:21:19] Found gzip - /bin/gzip
[09:21:19] Found vt - /usr/local/bin/vt
[09:21:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:21:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:21:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:21:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:21:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:21:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:21:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:21:19] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:21:20] Treating reference as 'fasta' format.
[09:21:20] Will use 1 CPU cores.
[09:21:20] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:21:20] Using read file: /corral4/main/objects/4/f/2/dataset_4f223e0c-0f27-465c-8f45-1036c8ca8fdb.dat
[09:21:20] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:20] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:20] Creating reference folder: reference
[09:21:20] Extracting FASTA and GFF from reference.
[09:21:27] Wrote 702 sequences to ref.fa
[09:21:27] Wrote 0 features to ref.gff
[09:21:28] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[09:21:28] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:28] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:21:28] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 4 | [12:48:03] This is snippy 4.6.0Show full stderr[12:48:03] This is snippy 4.6.0
[12:48:03] Written by Torsten Seemann
[12:48:03] Obtained from https://github.com/tseemann/snippy
[12:48:03] Detected operating system: linux
[12:48:03] Enabling bundled linux tools.
[12:48:03] Found bwa - /usr/local/bin/bwa
[12:48:03] Found bcftools - /usr/local/bin/bcftools
[12:48:03] Found samtools - /usr/local/bin/samtools
[12:48:03] Found java - /usr/local/bin/java
[12:48:03] Found snpEff - /usr/local/bin/snpEff
[12:48:03] Found samclip - /usr/local/bin/samclip
[12:48:03] Found seqtk - /usr/local/bin/seqtk
[12:48:03] Found parallel - /usr/local/bin/parallel
[12:48:03] Found freebayes - /usr/local/bin/freebayes
[12:48:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:48:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:48:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:48:03] Found vcfuniq - /usr/local/bin/vcfuniq
[12:48:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:48:03] Found gzip - /bin/gzip
[12:48:03] Found vt - /usr/local/bin/vt
[12:48:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:48:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:48:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:48:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:48:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:48:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:48:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:48:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [12:48:55] This is snippy 4.6.0Show full stderr[12:48:55] This is snippy 4.6.0
[12:48:55] Written by Torsten Seemann
[12:48:55] Obtained from https://github.com/tseemann/snippy
[12:48:55] Detected operating system: linux
[12:48:55] Enabling bundled linux tools.
[12:48:55] Found bwa - /usr/local/bin/bwa
[12:48:55] Found bcftools - /usr/local/bin/bcftools
[12:48:55] Found samtools - /usr/local/bin/samtools
[12:48:55] Found java - /usr/local/bin/java
[12:48:55] Found snpEff - /usr/local/bin/snpEff
[12:48:55] Found samclip - /usr/local/bin/samclip
[12:48:55] Found seqtk - /usr/local/bin/seqtk
[12:48:55] Found parallel - /usr/local/bin/parallel
[12:48:55] Found freebayes - /usr/local/bin/freebayes
[12:48:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:48:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:48:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:48:55] Found vcfuniq - /usr/local/bin/vcfuniq
[12:48:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:48:55] Found gzip - /bin/gzip
[12:48:55] Found vt - /usr/local/bin/vt
[12:48:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:48:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:48:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:48:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:48:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:48:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:48:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:48:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [19:40:25] This is snippy 4.6.0Show full stderr[19:40:25] This is snippy 4.6.0
[19:40:25] Written by Torsten Seemann
[19:40:25] Obtained from https://github.com/tseemann/snippy
[19:40:25] Detected operating system: linux
[19:40:25] Enabling bundled linux tools.
[19:40:25] Found bwa - /usr/local/bin/bwa
[19:40:25] Found bcftools - /usr/local/bin/bcftools
[19:40:25] Found samtools - /usr/local/bin/samtools
[19:40:25] Found java - /usr/local/bin/java
[19:40:25] Found snpEff - /usr/local/bin/snpEff
[19:40:25] Found samclip - /usr/local/bin/samclip
[19:40:25] Found seqtk - /usr/local/bin/seqtk
[19:40:25] Found parallel - /usr/local/bin/parallel
[19:40:25] Found freebayes - /usr/local/bin/freebayes
[19:40:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:25] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:25] Found gzip - /bin/gzip
[19:40:25] Found vt - /usr/local/bin/vt
[19:40:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [14:45:02] This is snippy 4.6.0Show full stderr[14:45:02] This is snippy 4.6.0
[14:45:02] Written by Torsten Seemann
[14:45:02] Obtained from https://github.com/tseemann/snippy
[14:45:02] Detected operating system: linux
[14:45:02] Enabling bundled linux tools.
[14:45:02] Found bwa - /usr/local/bin/bwa
[14:45:02] Found bcftools - /usr/local/bin/bcftools
[14:45:02] Found samtools - /usr/local/bin/samtools
[14:45:02] Found java - /usr/local/bin/java
[14:45:02] Found snpEff - /usr/local/bin/snpEff
[14:45:02] Found samclip - /usr/local/bin/samclip
[14:45:02] Found seqtk - /usr/local/bin/seqtk
[14:45:02] Found parallel - /usr/local/bin/parallel
[14:45:02] Found freebayes - /usr/local/bin/freebayes
[14:45:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:02] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:02] Found gzip - /bin/gzip
[14:45:02] Found vt - /usr/local/bin/vt
[14:45:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [14:47:12] This is snippy 4.6.0Show full stderr[14:47:12] This is snippy 4.6.0
[14:47:12] Written by Torsten Seemann
[14:47:12] Obtained from https://github.com/tseemann/snippy
[14:47:12] Detected operating system: linux
[14:47:12] Enabling bundled linux tools.
[14:47:12] Found bwa - /usr/local/bin/bwa
[14:47:12] Found bcftools - /usr/local/bin/bcftools
[14:47:12] Found samtools - /usr/local/bin/samtools
[14:47:12] Found java - /usr/local/bin/java
[14:47:12] Found snpEff - /usr/local/bin/snpEff
[14:47:12] Found samclip - /usr/local/bin/samclip
[14:47:12] Found seqtk - /usr/local/bin/seqtk
[14:47:12] Found parallel - /usr/local/bin/parallel
[14:47:12] Found freebayes - /usr/local/bin/freebayes
[14:47:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:47:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:47:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:47:12] Found vcfuniq - /usr/local/bin/vcfuniq
[14:47:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:47:12] Found gzip - /bin/gzip
[14:47:12] Found vt - /usr/local/bin/vt
[14:47:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:47:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:47:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:47:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:47:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:47:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:47:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:47:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [14:47:26] This is snippy 4.6.0Show full stderr[14:47:26] This is snippy 4.6.0
[14:47:26] Written by Torsten Seemann
[14:47:26] Obtained from https://github.com/tseemann/snippy
[14:47:26] Detected operating system: linux
[14:47:26] Enabling bundled linux tools.
[14:47:26] Found bwa - /usr/local/bin/bwa
[14:47:26] Found bcftools - /usr/local/bin/bcftools
[14:47:26] Found samtools - /usr/local/bin/samtools
[14:47:26] Found java - /usr/local/bin/java
[14:47:26] Found snpEff - /usr/local/bin/snpEff
[14:47:26] Found samclip - /usr/local/bin/samclip
[14:47:26] Found seqtk - /usr/local/bin/seqtk
[14:47:26] Found parallel - /usr/local/bin/parallel
[14:47:26] Found freebayes - /usr/local/bin/freebayes
[14:47:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:47:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:47:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:47:26] Found vcfuniq - /usr/local/bin/vcfuniq
[14:47:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:47:26] Found gzip - /bin/gzip
[14:47:26] Found vt - /usr/local/bin/vt
[14:47:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:47:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:47:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:47:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:47:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:47:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:47:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:47:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 4 | [17:38:33] This is snippy 4.6.0Show full stderr[17:38:33] This is snippy 4.6.0
[17:38:33] Written by Torsten Seemann
[17:38:33] Obtained from https://github.com/tseemann/snippy
[17:38:33] Detected operating system: linux
[17:38:33] Enabling bundled linux tools.
[17:38:33] Found bwa - /usr/local/bin/bwa
[17:38:33] Found bcftools - /usr/local/bin/bcftools
[17:38:33] Found samtools - /usr/local/bin/samtools
[17:38:33] Found java - /usr/local/bin/java
[17:38:33] Found snpEff - /usr/local/bin/snpEff
[17:38:33] Found samclip - /usr/local/bin/samclip
[17:38:33] Found seqtk - /usr/local/bin/seqtk
[17:38:33] Found parallel - /usr/local/bin/parallel
[17:38:33] Found freebayes - /usr/local/bin/freebayes
[17:38:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:38:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:38:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:38:33] Found vcfuniq - /usr/local/bin/vcfuniq
[17:38:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:38:33] Found gzip - /bin/gzip
[17:38:33] Found vt - /usr/local/bin/vt
[17:38:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:38:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:38:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:38:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:38:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:38:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:38:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:38:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [21:34:13] This is snippy 4.6.0Show full stderr[21:34:13] This is snippy 4.6.0
[21:34:13] Written by Torsten Seemann
[21:34:13] Obtained from https://github.com/tseemann/snippy
[21:34:13] Detected operating system: linux
[21:34:13] Enabling bundled linux tools.
[21:34:13] Found bwa - /usr/local/bin/bwa
[21:34:13] Found bcftools - /usr/local/bin/bcftools
[21:34:13] Found samtools - /usr/local/bin/samtools
[21:34:13] Found java - /usr/local/bin/java
[21:34:13] Found snpEff - /usr/local/bin/snpEff
[21:34:13] Found samclip - /usr/local/bin/samclip
[21:34:13] Found seqtk - /usr/local/bin/seqtk
[21:34:13] Found parallel - /usr/local/bin/parallel
[21:34:13] Found freebayes - /usr/local/bin/freebayes
[21:34:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:34:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:34:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:34:13] Found vcfuniq - /usr/local/bin/vcfuniq
[21:34:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:34:13] Found gzip - /bin/gzip
[21:34:13] Found vt - /usr/local/bin/vt
[21:34:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:34:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:34:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:34:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:34:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:34:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:34:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:34:15] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:34:15] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 3 | [21:34:28] This is snippy 4.6.0Show full stderr[21:34:28] This is snippy 4.6.0
[21:34:28] Written by Torsten Seemann
[21:34:28] Obtained from https://github.com/tseemann/snippy
[21:34:28] Detected operating system: linux
[21:34:28] Enabling bundled linux tools.
[21:34:28] Found bwa - /usr/local/bin/bwa
[21:34:28] Found bcftools - /usr/local/bin/bcftools
[21:34:28] Found samtools - /usr/local/bin/samtools
[21:34:28] Found java - /usr/local/bin/java
[21:34:28] Found snpEff - /usr/local/bin/snpEff
[21:34:28] Found samclip - /usr/local/bin/samclip
[21:34:28] Found seqtk - /usr/local/bin/seqtk
[21:34:28] Found parallel - /usr/local/bin/parallel
[21:34:28] Found freebayes - /usr/local/bin/freebayes
[21:34:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:34:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:34:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:34:28] Found vcfuniq - /usr/local/bin/vcfuniq
[21:34:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:34:28] Found gzip - /bin/gzip
[21:34:28] Found vt - /usr/local/bin/vt
[21:34:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:34:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:34:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:34:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:34:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:34:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:34:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:34:29] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:34:29] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 3 | [21:34:49] This is snippy 4.6.0Show full stderr[21:34:49] This is snippy 4.6.0
[21:34:49] Written by Torsten Seemann
[21:34:49] Obtained from https://github.com/tseemann/snippy
[21:34:49] Detected operating system: linux
[21:34:49] Enabling bundled linux tools.
[21:34:49] Found bwa - /usr/local/bin/bwa
[21:34:49] Found bcftools - /usr/local/bin/bcftools
[21:34:49] Found samtools - /usr/local/bin/samtools
[21:34:49] Found java - /usr/local/bin/java
[21:34:49] Found snpEff - /usr/local/bin/snpEff
[21:34:49] Found samclip - /usr/local/bin/samclip
[21:34:49] Found seqtk - /usr/local/bin/seqtk
[21:34:49] Found parallel - /usr/local/bin/parallel
[21:34:49] Found freebayes - /usr/local/bin/freebayes
[21:34:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:34:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:34:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:34:49] Found vcfuniq - /usr/local/bin/vcfuniq
[21:34:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:34:49] Found gzip - /bin/gzip
[21:34:49] Found vt - /usr/local/bin/vt
[21:34:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:34:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:34:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:34:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:34:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:34:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:34:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:34:50] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:34:50] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 3 | [04:37:53] This is snippy 4.6.0Show full stderr[04:37:53] This is snippy 4.6.0
[04:37:53] Written by Torsten Seemann
[04:37:53] Obtained from https://github.com/tseemann/snippy
[04:37:53] Detected operating system: linux
[04:37:53] Enabling bundled linux tools.
[04:37:53] Found bwa - /usr/local/bin/bwa
[04:37:53] Found bcftools - /usr/local/bin/bcftools
[04:37:53] Found samtools - /usr/local/bin/samtools
[04:37:53] Found java - /usr/local/bin/java
[04:37:53] Found snpEff - /usr/local/bin/snpEff
[04:37:53] Found samclip - /usr/local/bin/samclip
[04:37:53] Found seqtk - /usr/local/bin/seqtk
[04:37:53] Found parallel - /usr/local/bin/parallel
[04:37:53] Found freebayes - /usr/local/bin/freebayes
[04:37:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:53] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:53] Found gzip - /bin/gzip
[04:37:53] Found vt - /usr/local/bin/vt
[04:37:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:39:21] This is snippy 4.6.0Show full stderr[04:39:21] This is snippy 4.6.0
[04:39:21] Written by Torsten Seemann
[04:39:21] Obtained from https://github.com/tseemann/snippy
[04:39:21] Detected operating system: linux
[04:39:21] Enabling bundled linux tools.
[04:39:21] Found bwa - /usr/local/bin/bwa
[04:39:21] Found bcftools - /usr/local/bin/bcftools
[04:39:21] Found samtools - /usr/local/bin/samtools
[04:39:21] Found java - /usr/local/bin/java
[04:39:21] Found snpEff - /usr/local/bin/snpEff
[04:39:21] Found samclip - /usr/local/bin/samclip
[04:39:21] Found seqtk - /usr/local/bin/seqtk
[04:39:21] Found parallel - /usr/local/bin/parallel
[04:39:21] Found freebayes - /usr/local/bin/freebayes
[04:39:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:39:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:39:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:39:21] Found vcfuniq - /usr/local/bin/vcfuniq
[04:39:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:39:21] Found gzip - /bin/gzip
[04:39:21] Found vt - /usr/local/bin/vt
[04:39:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:39:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:39:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:39:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:39:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:39:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:39:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:39:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:37:27] This is snippy 4.6.0Show full stderr[04:37:27] This is snippy 4.6.0
[04:37:27] Written by Torsten Seemann
[04:37:27] Obtained from https://github.com/tseemann/snippy
[04:37:27] Detected operating system: linux
[04:37:27] Enabling bundled linux tools.
[04:37:27] Found bwa - /usr/local/bin/bwa
[04:37:27] Found bcftools - /usr/local/bin/bcftools
[04:37:27] Found samtools - /usr/local/bin/samtools
[04:37:27] Found java - /usr/local/bin/java
[04:37:27] Found snpEff - /usr/local/bin/snpEff
[04:37:27] Found samclip - /usr/local/bin/samclip
[04:37:27] Found seqtk - /usr/local/bin/seqtk
[04:37:27] Found parallel - /usr/local/bin/parallel
[04:37:27] Found freebayes - /usr/local/bin/freebayes
[04:37:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:27] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:27] Found gzip - /bin/gzip
[04:37:27] Found vt - /usr/local/bin/vt
[04:37:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:37:59] This is snippy 4.6.0Show full stderr[04:37:59] This is snippy 4.6.0
[04:37:59] Written by Torsten Seemann
[04:37:59] Obtained from https://github.com/tseemann/snippy
[04:37:59] Detected operating system: linux
[04:37:59] Enabling bundled linux tools.
[04:37:59] Found bwa - /usr/local/bin/bwa
[04:37:59] Found bcftools - /usr/local/bin/bcftools
[04:37:59] Found samtools - /usr/local/bin/samtools
[04:37:59] Found java - /usr/local/bin/java
[04:37:59] Found snpEff - /usr/local/bin/snpEff
[04:37:59] Found samclip - /usr/local/bin/samclip
[04:37:59] Found seqtk - /usr/local/bin/seqtk
[04:37:59] Found parallel - /usr/local/bin/parallel
[04:37:59] Found freebayes - /usr/local/bin/freebayes
[04:37:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:59] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:59] Found gzip - /bin/gzip
[04:37:59] Found vt - /usr/local/bin/vt
[04:37:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:39:57] This is snippy 4.6.0Show full stderr[04:39:57] This is snippy 4.6.0
[04:39:57] Written by Torsten Seemann
[04:39:57] Obtained from https://github.com/tseemann/snippy
[04:39:57] Detected operating system: linux
[04:39:57] Enabling bundled linux tools.
[04:39:57] Found bwa - /usr/local/bin/bwa
[04:39:57] Found bcftools - /usr/local/bin/bcftools
[04:39:57] Found samtools - /usr/local/bin/samtools
[04:39:57] Found java - /usr/local/bin/java
[04:39:57] Found snpEff - /usr/local/bin/snpEff
[04:39:57] Found samclip - /usr/local/bin/samclip
[04:39:57] Found seqtk - /usr/local/bin/seqtk
[04:39:57] Found parallel - /usr/local/bin/parallel
[04:39:57] Found freebayes - /usr/local/bin/freebayes
[04:39:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:39:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:39:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:39:57] Found vcfuniq - /usr/local/bin/vcfuniq
[04:39:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:39:57] Found gzip - /bin/gzip
[04:39:57] Found vt - /usr/local/bin/vt
[04:39:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:39:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:39:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:39:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:39:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:39:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:39:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:39:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:37:15] This is snippy 4.6.0Show full stderr[04:37:15] This is snippy 4.6.0
[04:37:15] Written by Torsten Seemann
[04:37:15] Obtained from https://github.com/tseemann/snippy
[04:37:15] Detected operating system: linux
[04:37:15] Enabling bundled linux tools.
[04:37:15] Found bwa - /usr/local/bin/bwa
[04:37:15] Found bcftools - /usr/local/bin/bcftools
[04:37:15] Found samtools - /usr/local/bin/samtools
[04:37:15] Found java - /usr/local/bin/java
[04:37:15] Found snpEff - /usr/local/bin/snpEff
[04:37:15] Found samclip - /usr/local/bin/samclip
[04:37:15] Found seqtk - /usr/local/bin/seqtk
[04:37:15] Found parallel - /usr/local/bin/parallel
[04:37:15] Found freebayes - /usr/local/bin/freebayes
[04:37:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:15] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:15] Found gzip - /bin/gzip
[04:37:15] Found vt - /usr/local/bin/vt
[04:37:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:39:39] This is snippy 4.6.0Show full stderr[04:39:39] This is snippy 4.6.0
[04:39:39] Written by Torsten Seemann
[04:39:39] Obtained from https://github.com/tseemann/snippy
[04:39:39] Detected operating system: linux
[04:39:39] Enabling bundled linux tools.
[04:39:39] Found bwa - /usr/local/bin/bwa
[04:39:39] Found bcftools - /usr/local/bin/bcftools
[04:39:39] Found samtools - /usr/local/bin/samtools
[04:39:39] Found java - /usr/local/bin/java
[04:39:39] Found snpEff - /usr/local/bin/snpEff
[04:39:39] Found samclip - /usr/local/bin/samclip
[04:39:39] Found seqtk - /usr/local/bin/seqtk
[04:39:39] Found parallel - /usr/local/bin/parallel
[04:39:39] Found freebayes - /usr/local/bin/freebayes
[04:39:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:39:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:39:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:39:39] Found vcfuniq - /usr/local/bin/vcfuniq
[04:39:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:39:39] Found gzip - /bin/gzip
[04:39:39] Found vt - /usr/local/bin/vt
[04:39:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:39:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:39:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:39:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:39:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:39:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:39:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:39:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:40:29] This is snippy 4.6.0Show full stderr[04:40:29] This is snippy 4.6.0
[04:40:29] Written by Torsten Seemann
[04:40:29] Obtained from https://github.com/tseemann/snippy
[04:40:29] Detected operating system: linux
[04:40:29] Enabling bundled linux tools.
[04:40:29] Found bwa - /usr/local/bin/bwa
[04:40:29] Found bcftools - /usr/local/bin/bcftools
[04:40:29] Found samtools - /usr/local/bin/samtools
[04:40:29] Found java - /usr/local/bin/java
[04:40:29] Found snpEff - /usr/local/bin/snpEff
[04:40:29] Found samclip - /usr/local/bin/samclip
[04:40:29] Found seqtk - /usr/local/bin/seqtk
[04:40:29] Found parallel - /usr/local/bin/parallel
[04:40:29] Found freebayes - /usr/local/bin/freebayes
[04:40:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:29] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:29] Found gzip - /bin/gzip
[04:40:29] Found vt - /usr/local/bin/vt
[04:40:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:40:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:40:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:40:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:39:24] This is snippy 4.6.0Show full stderr[04:39:24] This is snippy 4.6.0
[04:39:24] Written by Torsten Seemann
[04:39:24] Obtained from https://github.com/tseemann/snippy
[04:39:24] Detected operating system: linux
[04:39:24] Enabling bundled linux tools.
[04:39:24] Found bwa - /usr/local/bin/bwa
[04:39:24] Found bcftools - /usr/local/bin/bcftools
[04:39:24] Found samtools - /usr/local/bin/samtools
[04:39:24] Found java - /usr/local/bin/java
[04:39:24] Found snpEff - /usr/local/bin/snpEff
[04:39:24] Found samclip - /usr/local/bin/samclip
[04:39:24] Found seqtk - /usr/local/bin/seqtk
[04:39:24] Found parallel - /usr/local/bin/parallel
[04:39:24] Found freebayes - /usr/local/bin/freebayes
[04:39:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:39:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:39:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:39:24] Found vcfuniq - /usr/local/bin/vcfuniq
[04:39:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:39:24] Found gzip - /bin/gzip
[04:39:24] Found vt - /usr/local/bin/vt
[04:39:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:39:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:39:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:39:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:39:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:39:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:39:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:39:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:40:44] This is snippy 4.6.0Show full stderr[04:40:44] This is snippy 4.6.0
[04:40:44] Written by Torsten Seemann
[04:40:44] Obtained from https://github.com/tseemann/snippy
[04:40:44] Detected operating system: linux
[04:40:44] Enabling bundled linux tools.
[04:40:44] Found bwa - /usr/local/bin/bwa
[04:40:44] Found bcftools - /usr/local/bin/bcftools
[04:40:44] Found samtools - /usr/local/bin/samtools
[04:40:44] Found java - /usr/local/bin/java
[04:40:44] Found snpEff - /usr/local/bin/snpEff
[04:40:44] Found samclip - /usr/local/bin/samclip
[04:40:44] Found seqtk - /usr/local/bin/seqtk
[04:40:44] Found parallel - /usr/local/bin/parallel
[04:40:44] Found freebayes - /usr/local/bin/freebayes
[04:40:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:44] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:44] Found gzip - /bin/gzip
[04:40:44] Found vt - /usr/local/bin/vt
[04:40:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:40:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:40:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:40:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:40:56] This is snippy 4.6.0Show full stderr[04:40:56] This is snippy 4.6.0
[04:40:56] Written by Torsten Seemann
[04:40:56] Obtained from https://github.com/tseemann/snippy
[04:40:56] Detected operating system: linux
[04:40:56] Enabling bundled linux tools.
[04:40:56] Found bwa - /usr/local/bin/bwa
[04:40:56] Found bcftools - /usr/local/bin/bcftools
[04:40:56] Found samtools - /usr/local/bin/samtools
[04:40:56] Found java - /usr/local/bin/java
[04:40:56] Found snpEff - /usr/local/bin/snpEff
[04:40:56] Found samclip - /usr/local/bin/samclip
[04:40:56] Found seqtk - /usr/local/bin/seqtk
[04:40:56] Found parallel - /usr/local/bin/parallel
[04:40:56] Found freebayes - /usr/local/bin/freebayes
[04:40:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:56] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:56] Found gzip - /bin/gzip
[04:40:56] Found vt - /usr/local/bin/vt
[04:40:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:40:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:40:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:40:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:41:09] This is snippy 4.6.0Show full stderr[04:41:09] This is snippy 4.6.0
[04:41:09] Written by Torsten Seemann
[04:41:09] Obtained from https://github.com/tseemann/snippy
[04:41:09] Detected operating system: linux
[04:41:09] Enabling bundled linux tools.
[04:41:09] Found bwa - /usr/local/bin/bwa
[04:41:09] Found bcftools - /usr/local/bin/bcftools
[04:41:09] Found samtools - /usr/local/bin/samtools
[04:41:09] Found java - /usr/local/bin/java
[04:41:09] Found snpEff - /usr/local/bin/snpEff
[04:41:09] Found samclip - /usr/local/bin/samclip
[04:41:09] Found seqtk - /usr/local/bin/seqtk
[04:41:09] Found parallel - /usr/local/bin/parallel
[04:41:09] Found freebayes - /usr/local/bin/freebayes
[04:41:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:09] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:09] Found gzip - /bin/gzip
[04:41:09] Found vt - /usr/local/bin/vt
[04:41:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:41:24] This is snippy 4.6.0Show full stderr[04:41:24] This is snippy 4.6.0
[04:41:24] Written by Torsten Seemann
[04:41:24] Obtained from https://github.com/tseemann/snippy
[04:41:24] Detected operating system: linux
[04:41:24] Enabling bundled linux tools.
[04:41:24] Found bwa - /usr/local/bin/bwa
[04:41:24] Found bcftools - /usr/local/bin/bcftools
[04:41:24] Found samtools - /usr/local/bin/samtools
[04:41:24] Found java - /usr/local/bin/java
[04:41:24] Found snpEff - /usr/local/bin/snpEff
[04:41:24] Found samclip - /usr/local/bin/samclip
[04:41:24] Found seqtk - /usr/local/bin/seqtk
[04:41:24] Found parallel - /usr/local/bin/parallel
[04:41:24] Found freebayes - /usr/local/bin/freebayes
[04:41:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:24] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:24] Found gzip - /bin/gzip
[04:41:24] Found vt - /usr/local/bin/vt
[04:41:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:42:21] This is snippy 4.6.0Show full stderr[04:42:21] This is snippy 4.6.0
[04:42:21] Written by Torsten Seemann
[04:42:21] Obtained from https://github.com/tseemann/snippy
[04:42:21] Detected operating system: linux
[04:42:21] Enabling bundled linux tools.
[04:42:21] Found bwa - /usr/local/bin/bwa
[04:42:21] Found bcftools - /usr/local/bin/bcftools
[04:42:21] Found samtools - /usr/local/bin/samtools
[04:42:21] Found java - /usr/local/bin/java
[04:42:21] Found snpEff - /usr/local/bin/snpEff
[04:42:21] Found samclip - /usr/local/bin/samclip
[04:42:21] Found seqtk - /usr/local/bin/seqtk
[04:42:21] Found parallel - /usr/local/bin/parallel
[04:42:21] Found freebayes - /usr/local/bin/freebayes
[04:42:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:21] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:21] Found gzip - /bin/gzip
[04:42:21] Found vt - /usr/local/bin/vt
[04:42:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:41:46] This is snippy 4.6.0Show full stderr[04:41:46] This is snippy 4.6.0
[04:41:46] Written by Torsten Seemann
[04:41:46] Obtained from https://github.com/tseemann/snippy
[04:41:46] Detected operating system: linux
[04:41:46] Enabling bundled linux tools.
[04:41:46] Found bwa - /usr/local/bin/bwa
[04:41:46] Found bcftools - /usr/local/bin/bcftools
[04:41:46] Found samtools - /usr/local/bin/samtools
[04:41:46] Found java - /usr/local/bin/java
[04:41:46] Found snpEff - /usr/local/bin/snpEff
[04:41:46] Found samclip - /usr/local/bin/samclip
[04:41:46] Found seqtk - /usr/local/bin/seqtk
[04:41:46] Found parallel - /usr/local/bin/parallel
[04:41:46] Found freebayes - /usr/local/bin/freebayes
[04:41:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:46] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:46] Found gzip - /bin/gzip
[04:41:46] Found vt - /usr/local/bin/vt
[04:41:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:43:03] This is snippy 4.6.0Show full stderr[04:43:03] This is snippy 4.6.0
[04:43:03] Written by Torsten Seemann
[04:43:03] Obtained from https://github.com/tseemann/snippy
[04:43:03] Detected operating system: linux
[04:43:03] Enabling bundled linux tools.
[04:43:03] Found bwa - /usr/local/bin/bwa
[04:43:03] Found bcftools - /usr/local/bin/bcftools
[04:43:03] Found samtools - /usr/local/bin/samtools
[04:43:03] Found java - /usr/local/bin/java
[04:43:03] Found snpEff - /usr/local/bin/snpEff
[04:43:03] Found samclip - /usr/local/bin/samclip
[04:43:03] Found seqtk - /usr/local/bin/seqtk
[04:43:03] Found parallel - /usr/local/bin/parallel
[04:43:03] Found freebayes - /usr/local/bin/freebayes
[04:43:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:03] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:03] Found gzip - /bin/gzip
[04:43:03] Found vt - /usr/local/bin/vt
[04:43:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:44:46] This is snippy 4.6.0Show full stderr[04:44:46] This is snippy 4.6.0
[04:44:46] Written by Torsten Seemann
[04:44:46] Obtained from https://github.com/tseemann/snippy
[04:44:46] Detected operating system: linux
[04:44:46] Enabling bundled linux tools.
[04:44:46] Found bwa - /usr/local/bin/bwa
[04:44:46] Found bcftools - /usr/local/bin/bcftools
[04:44:46] Found samtools - /usr/local/bin/samtools
[04:44:46] Found java - /usr/local/bin/java
[04:44:46] Found snpEff - /usr/local/bin/snpEff
[04:44:46] Found samclip - /usr/local/bin/samclip
[04:44:46] Found seqtk - /usr/local/bin/seqtk
[04:44:46] Found parallel - /usr/local/bin/parallel
[04:44:46] Found freebayes - /usr/local/bin/freebayes
[04:44:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:46] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:46] Found gzip - /bin/gzip
[04:44:46] Found vt - /usr/local/bin/vt
[04:44:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:43:24] This is snippy 4.6.0Show full stderr[04:43:24] This is snippy 4.6.0
[04:43:24] Written by Torsten Seemann
[04:43:24] Obtained from https://github.com/tseemann/snippy
[04:43:24] Detected operating system: linux
[04:43:24] Enabling bundled linux tools.
[04:43:24] Found bwa - /usr/local/bin/bwa
[04:43:24] Found bcftools - /usr/local/bin/bcftools
[04:43:24] Found samtools - /usr/local/bin/samtools
[04:43:24] Found java - /usr/local/bin/java
[04:43:24] Found snpEff - /usr/local/bin/snpEff
[04:43:24] Found samclip - /usr/local/bin/samclip
[04:43:24] Found seqtk - /usr/local/bin/seqtk
[04:43:24] Found parallel - /usr/local/bin/parallel
[04:43:24] Found freebayes - /usr/local/bin/freebayes
[04:43:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:24] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:24] Found gzip - /bin/gzip
[04:43:24] Found vt - /usr/local/bin/vt
[04:43:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:43:21] This is snippy 4.6.0Show full stderr[04:43:21] This is snippy 4.6.0
[04:43:21] Written by Torsten Seemann
[04:43:21] Obtained from https://github.com/tseemann/snippy
[04:43:21] Detected operating system: linux
[04:43:21] Enabling bundled linux tools.
[04:43:21] Found bwa - /usr/local/bin/bwa
[04:43:21] Found bcftools - /usr/local/bin/bcftools
[04:43:21] Found samtools - /usr/local/bin/samtools
[04:43:21] Found java - /usr/local/bin/java
[04:43:21] Found snpEff - /usr/local/bin/snpEff
[04:43:21] Found samclip - /usr/local/bin/samclip
[04:43:21] Found seqtk - /usr/local/bin/seqtk
[04:43:21] Found parallel - /usr/local/bin/parallel
[04:43:21] Found freebayes - /usr/local/bin/freebayes
[04:43:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:21] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:21] Found gzip - /bin/gzip
[04:43:21] Found vt - /usr/local/bin/vt
[04:43:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:55:03] This is snippy 4.6.0Show full stderr[04:55:03] This is snippy 4.6.0
[04:55:03] Written by Torsten Seemann
[04:55:03] Obtained from https://github.com/tseemann/snippy
[04:55:03] Detected operating system: linux
[04:55:03] Enabling bundled linux tools.
[04:55:03] Found bwa - /usr/local/bin/bwa
[04:55:03] Found bcftools - /usr/local/bin/bcftools
[04:55:03] Found samtools - /usr/local/bin/samtools
[04:55:03] Found java - /usr/local/bin/java
[04:55:03] Found snpEff - /usr/local/bin/snpEff
[04:55:03] Found samclip - /usr/local/bin/samclip
[04:55:03] Found seqtk - /usr/local/bin/seqtk
[04:55:03] Found parallel - /usr/local/bin/parallel
[04:55:03] Found freebayes - /usr/local/bin/freebayes
[04:55:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:03] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:03] Found gzip - /bin/gzip
[04:55:03] Found vt - /usr/local/bin/vt
[04:55:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:55:46] This is snippy 4.6.0Show full stderr[04:55:46] This is snippy 4.6.0
[04:55:46] Written by Torsten Seemann
[04:55:46] Obtained from https://github.com/tseemann/snippy
[04:55:46] Detected operating system: linux
[04:55:46] Enabling bundled linux tools.
[04:55:46] Found bwa - /usr/local/bin/bwa
[04:55:46] Found bcftools - /usr/local/bin/bcftools
[04:55:46] Found samtools - /usr/local/bin/samtools
[04:55:46] Found java - /usr/local/bin/java
[04:55:46] Found snpEff - /usr/local/bin/snpEff
[04:55:46] Found samclip - /usr/local/bin/samclip
[04:55:46] Found seqtk - /usr/local/bin/seqtk
[04:55:46] Found parallel - /usr/local/bin/parallel
[04:55:46] Found freebayes - /usr/local/bin/freebayes
[04:55:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:46] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:46] Found gzip - /bin/gzip
[04:55:46] Found vt - /usr/local/bin/vt
[04:55:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:55:18] This is snippy 4.6.0Show full stderr[04:55:18] This is snippy 4.6.0
[04:55:18] Written by Torsten Seemann
[04:55:18] Obtained from https://github.com/tseemann/snippy
[04:55:18] Detected operating system: linux
[04:55:18] Enabling bundled linux tools.
[04:55:18] Found bwa - /usr/local/bin/bwa
[04:55:18] Found bcftools - /usr/local/bin/bcftools
[04:55:18] Found samtools - /usr/local/bin/samtools
[04:55:18] Found java - /usr/local/bin/java
[04:55:18] Found snpEff - /usr/local/bin/snpEff
[04:55:18] Found samclip - /usr/local/bin/samclip
[04:55:18] Found seqtk - /usr/local/bin/seqtk
[04:55:18] Found parallel - /usr/local/bin/parallel
[04:55:18] Found freebayes - /usr/local/bin/freebayes
[04:55:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:18] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:18] Found gzip - /bin/gzip
[04:55:18] Found vt - /usr/local/bin/vt
[04:55:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:55:33] This is snippy 4.6.0Show full stderr[04:55:33] This is snippy 4.6.0
[04:55:33] Written by Torsten Seemann
[04:55:33] Obtained from https://github.com/tseemann/snippy
[04:55:33] Detected operating system: linux
[04:55:33] Enabling bundled linux tools.
[04:55:33] Found bwa - /usr/local/bin/bwa
[04:55:33] Found bcftools - /usr/local/bin/bcftools
[04:55:33] Found samtools - /usr/local/bin/samtools
[04:55:33] Found java - /usr/local/bin/java
[04:55:33] Found snpEff - /usr/local/bin/snpEff
[04:55:33] Found samclip - /usr/local/bin/samclip
[04:55:33] Found seqtk - /usr/local/bin/seqtk
[04:55:33] Found parallel - /usr/local/bin/parallel
[04:55:33] Found freebayes - /usr/local/bin/freebayes
[04:55:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:33] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:33] Found gzip - /bin/gzip
[04:55:33] Found vt - /usr/local/bin/vt
[04:55:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:56:42] This is snippy 4.6.0Show full stderr[04:56:42] This is snippy 4.6.0
[04:56:42] Written by Torsten Seemann
[04:56:42] Obtained from https://github.com/tseemann/snippy
[04:56:42] Detected operating system: linux
[04:56:42] Enabling bundled linux tools.
[04:56:42] Found bwa - /usr/local/bin/bwa
[04:56:42] Found bcftools - /usr/local/bin/bcftools
[04:56:42] Found samtools - /usr/local/bin/samtools
[04:56:42] Found java - /usr/local/bin/java
[04:56:42] Found snpEff - /usr/local/bin/snpEff
[04:56:42] Found samclip - /usr/local/bin/samclip
[04:56:42] Found seqtk - /usr/local/bin/seqtk
[04:56:42] Found parallel - /usr/local/bin/parallel
[04:56:42] Found freebayes - /usr/local/bin/freebayes
[04:56:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:42] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:42] Found gzip - /bin/gzip
[04:56:42] Found vt - /usr/local/bin/vt
[04:56:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:58:06] This is snippy 4.6.0Show full stderr[04:58:06] This is snippy 4.6.0
[04:58:06] Written by Torsten Seemann
[04:58:06] Obtained from https://github.com/tseemann/snippy
[04:58:06] Detected operating system: linux
[04:58:06] Enabling bundled linux tools.
[04:58:06] Found bwa - /usr/local/bin/bwa
[04:58:06] Found bcftools - /usr/local/bin/bcftools
[04:58:06] Found samtools - /usr/local/bin/samtools
[04:58:06] Found java - /usr/local/bin/java
[04:58:06] Found snpEff - /usr/local/bin/snpEff
[04:58:06] Found samclip - /usr/local/bin/samclip
[04:58:06] Found seqtk - /usr/local/bin/seqtk
[04:58:06] Found parallel - /usr/local/bin/parallel
[04:58:06] Found freebayes - /usr/local/bin/freebayes
[04:58:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:58:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:58:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:58:06] Found vcfuniq - /usr/local/bin/vcfuniq
[04:58:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:58:06] Found gzip - /bin/gzip
[04:58:06] Found vt - /usr/local/bin/vt
[04:58:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:58:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:58:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:58:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:58:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:58:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:58:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:58:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:57:51] This is snippy 4.6.0Show full stderr[04:57:51] This is snippy 4.6.0
[04:57:51] Written by Torsten Seemann
[04:57:51] Obtained from https://github.com/tseemann/snippy
[04:57:51] Detected operating system: linux
[04:57:51] Enabling bundled linux tools.
[04:57:51] Found bwa - /usr/local/bin/bwa
[04:57:51] Found bcftools - /usr/local/bin/bcftools
[04:57:51] Found samtools - /usr/local/bin/samtools
[04:57:51] Found java - /usr/local/bin/java
[04:57:51] Found snpEff - /usr/local/bin/snpEff
[04:57:51] Found samclip - /usr/local/bin/samclip
[04:57:51] Found seqtk - /usr/local/bin/seqtk
[04:57:51] Found parallel - /usr/local/bin/parallel
[04:57:51] Found freebayes - /usr/local/bin/freebayes
[04:57:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:51] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:51] Found gzip - /bin/gzip
[04:57:51] Found vt - /usr/local/bin/vt
[04:57:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:57:39] This is snippy 4.6.0Show full stderr[04:57:39] This is snippy 4.6.0
[04:57:39] Written by Torsten Seemann
[04:57:39] Obtained from https://github.com/tseemann/snippy
[04:57:39] Detected operating system: linux
[04:57:39] Enabling bundled linux tools.
[04:57:39] Found bwa - /usr/local/bin/bwa
[04:57:39] Found bcftools - /usr/local/bin/bcftools
[04:57:39] Found samtools - /usr/local/bin/samtools
[04:57:39] Found java - /usr/local/bin/java
[04:57:39] Found snpEff - /usr/local/bin/snpEff
[04:57:39] Found samclip - /usr/local/bin/samclip
[04:57:39] Found seqtk - /usr/local/bin/seqtk
[04:57:39] Found parallel - /usr/local/bin/parallel
[04:57:39] Found freebayes - /usr/local/bin/freebayes
[04:57:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:39] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:39] Found gzip - /bin/gzip
[04:57:39] Found vt - /usr/local/bin/vt
[04:57:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:00:30] This is snippy 4.6.0Show full stderr[05:00:30] This is snippy 4.6.0
[05:00:30] Written by Torsten Seemann
[05:00:30] Obtained from https://github.com/tseemann/snippy
[05:00:30] Detected operating system: linux
[05:00:30] Enabling bundled linux tools.
[05:00:30] Found bwa - /usr/local/bin/bwa
[05:00:30] Found bcftools - /usr/local/bin/bcftools
[05:00:30] Found samtools - /usr/local/bin/samtools
[05:00:30] Found java - /usr/local/bin/java
[05:00:30] Found snpEff - /usr/local/bin/snpEff
[05:00:30] Found samclip - /usr/local/bin/samclip
[05:00:30] Found seqtk - /usr/local/bin/seqtk
[05:00:30] Found parallel - /usr/local/bin/parallel
[05:00:30] Found freebayes - /usr/local/bin/freebayes
[05:00:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:30] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:30] Found gzip - /bin/gzip
[05:00:30] Found vt - /usr/local/bin/vt
[05:00:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:00:45] This is snippy 4.6.0Show full stderr[05:00:45] This is snippy 4.6.0
[05:00:45] Written by Torsten Seemann
[05:00:45] Obtained from https://github.com/tseemann/snippy
[05:00:45] Detected operating system: linux
[05:00:45] Enabling bundled linux tools.
[05:00:45] Found bwa - /usr/local/bin/bwa
[05:00:45] Found bcftools - /usr/local/bin/bcftools
[05:00:45] Found samtools - /usr/local/bin/samtools
[05:00:45] Found java - /usr/local/bin/java
[05:00:45] Found snpEff - /usr/local/bin/snpEff
[05:00:45] Found samclip - /usr/local/bin/samclip
[05:00:45] Found seqtk - /usr/local/bin/seqtk
[05:00:45] Found parallel - /usr/local/bin/parallel
[05:00:45] Found freebayes - /usr/local/bin/freebayes
[05:00:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:45] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:45] Found gzip - /bin/gzip
[05:00:45] Found vt - /usr/local/bin/vt
[05:00:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:01:00] This is snippy 4.6.0Show full stderr[05:01:00] This is snippy 4.6.0
[05:01:00] Written by Torsten Seemann
[05:01:00] Obtained from https://github.com/tseemann/snippy
[05:01:00] Detected operating system: linux
[05:01:00] Enabling bundled linux tools.
[05:01:00] Found bwa - /usr/local/bin/bwa
[05:01:00] Found bcftools - /usr/local/bin/bcftools
[05:01:00] Found samtools - /usr/local/bin/samtools
[05:01:00] Found java - /usr/local/bin/java
[05:01:00] Found snpEff - /usr/local/bin/snpEff
[05:01:00] Found samclip - /usr/local/bin/samclip
[05:01:00] Found seqtk - /usr/local/bin/seqtk
[05:01:00] Found parallel - /usr/local/bin/parallel
[05:01:00] Found freebayes - /usr/local/bin/freebayes
[05:01:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:00] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:00] Found gzip - /bin/gzip
[05:01:00] Found vt - /usr/local/bin/vt
[05:01:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:01:31] This is snippy 4.6.0Show full stderr[05:01:31] This is snippy 4.6.0
[05:01:31] Written by Torsten Seemann
[05:01:31] Obtained from https://github.com/tseemann/snippy
[05:01:31] Detected operating system: linux
[05:01:31] Enabling bundled linux tools.
[05:01:31] Found bwa - /usr/local/bin/bwa
[05:01:31] Found bcftools - /usr/local/bin/bcftools
[05:01:31] Found samtools - /usr/local/bin/samtools
[05:01:31] Found java - /usr/local/bin/java
[05:01:31] Found snpEff - /usr/local/bin/snpEff
[05:01:31] Found samclip - /usr/local/bin/samclip
[05:01:31] Found seqtk - /usr/local/bin/seqtk
[05:01:31] Found parallel - /usr/local/bin/parallel
[05:01:31] Found freebayes - /usr/local/bin/freebayes
[05:01:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:31] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:31] Found gzip - /bin/gzip
[05:01:31] Found vt - /usr/local/bin/vt
[05:01:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:58:54] This is snippy 4.6.0Show full stderr[04:58:54] This is snippy 4.6.0
[04:58:54] Written by Torsten Seemann
[04:58:54] Obtained from https://github.com/tseemann/snippy
[04:58:54] Detected operating system: linux
[04:58:54] Enabling bundled linux tools.
[04:58:54] Found bwa - /usr/local/bin/bwa
[04:58:54] Found bcftools - /usr/local/bin/bcftools
[04:58:54] Found samtools - /usr/local/bin/samtools
[04:58:54] Found java - /usr/local/bin/java
[04:58:54] Found snpEff - /usr/local/bin/snpEff
[04:58:54] Found samclip - /usr/local/bin/samclip
[04:58:54] Found seqtk - /usr/local/bin/seqtk
[04:58:54] Found parallel - /usr/local/bin/parallel
[04:58:54] Found freebayes - /usr/local/bin/freebayes
[04:58:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:58:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:58:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:58:54] Found vcfuniq - /usr/local/bin/vcfuniq
[04:58:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:58:54] Found gzip - /bin/gzip
[04:58:54] Found vt - /usr/local/bin/vt
[04:58:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:58:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:58:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:58:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:58:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:58:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:58:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:58:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:02:08] This is snippy 4.6.0Show full stderr[05:02:08] This is snippy 4.6.0
[05:02:08] Written by Torsten Seemann
[05:02:08] Obtained from https://github.com/tseemann/snippy
[05:02:08] Detected operating system: linux
[05:02:08] Enabling bundled linux tools.
[05:02:08] Found bwa - /usr/local/bin/bwa
[05:02:08] Found bcftools - /usr/local/bin/bcftools
[05:02:08] Found samtools - /usr/local/bin/samtools
[05:02:08] Found java - /usr/local/bin/java
[05:02:08] Found snpEff - /usr/local/bin/snpEff
[05:02:08] Found samclip - /usr/local/bin/samclip
[05:02:08] Found seqtk - /usr/local/bin/seqtk
[05:02:08] Found parallel - /usr/local/bin/parallel
[05:02:08] Found freebayes - /usr/local/bin/freebayes
[05:02:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:08] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:08] Found gzip - /bin/gzip
[05:02:08] Found vt - /usr/local/bin/vt
[05:02:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:03:32] This is snippy 4.6.0Show full stderr[05:03:32] This is snippy 4.6.0
[05:03:32] Written by Torsten Seemann
[05:03:32] Obtained from https://github.com/tseemann/snippy
[05:03:32] Detected operating system: linux
[05:03:32] Enabling bundled linux tools.
[05:03:32] Found bwa - /usr/local/bin/bwa
[05:03:32] Found bcftools - /usr/local/bin/bcftools
[05:03:32] Found samtools - /usr/local/bin/samtools
[05:03:32] Found java - /usr/local/bin/java
[05:03:32] Found snpEff - /usr/local/bin/snpEff
[05:03:32] Found samclip - /usr/local/bin/samclip
[05:03:32] Found seqtk - /usr/local/bin/seqtk
[05:03:32] Found parallel - /usr/local/bin/parallel
[05:03:32] Found freebayes - /usr/local/bin/freebayes
[05:03:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:32] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:32] Found gzip - /bin/gzip
[05:03:32] Found vt - /usr/local/bin/vt
[05:03:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:02:34] This is snippy 4.6.0Show full stderr[05:02:34] This is snippy 4.6.0
[05:02:34] Written by Torsten Seemann
[05:02:34] Obtained from https://github.com/tseemann/snippy
[05:02:34] Detected operating system: linux
[05:02:34] Enabling bundled linux tools.
[05:02:34] Found bwa - /usr/local/bin/bwa
[05:02:34] Found bcftools - /usr/local/bin/bcftools
[05:02:34] Found samtools - /usr/local/bin/samtools
[05:02:34] Found java - /usr/local/bin/java
[05:02:34] Found snpEff - /usr/local/bin/snpEff
[05:02:34] Found samclip - /usr/local/bin/samclip
[05:02:35] Found seqtk - /usr/local/bin/seqtk
[05:02:35] Found parallel - /usr/local/bin/parallel
[05:02:35] Found freebayes - /usr/local/bin/freebayes
[05:02:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:35] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:35] Found gzip - /bin/gzip
[05:02:35] Found vt - /usr/local/bin/vt
[05:02:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:04:02] This is snippy 4.6.0Show full stderr[05:04:02] This is snippy 4.6.0
[05:04:02] Written by Torsten Seemann
[05:04:02] Obtained from https://github.com/tseemann/snippy
[05:04:02] Detected operating system: linux
[05:04:02] Enabling bundled linux tools.
[05:04:02] Found bwa - /usr/local/bin/bwa
[05:04:02] Found bcftools - /usr/local/bin/bcftools
[05:04:02] Found samtools - /usr/local/bin/samtools
[05:04:02] Found java - /usr/local/bin/java
[05:04:02] Found snpEff - /usr/local/bin/snpEff
[05:04:02] Found samclip - /usr/local/bin/samclip
[05:04:02] Found seqtk - /usr/local/bin/seqtk
[05:04:02] Found parallel - /usr/local/bin/parallel
[05:04:02] Found freebayes - /usr/local/bin/freebayes
[05:04:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:02] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:02] Found gzip - /bin/gzip
[05:04:02] Found vt - /usr/local/bin/vt
[05:04:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:05:02] This is snippy 4.6.0Show full stderr[05:05:02] This is snippy 4.6.0
[05:05:02] Written by Torsten Seemann
[05:05:02] Obtained from https://github.com/tseemann/snippy
[05:05:02] Detected operating system: linux
[05:05:02] Enabling bundled linux tools.
[05:05:02] Found bwa - /usr/local/bin/bwa
[05:05:02] Found bcftools - /usr/local/bin/bcftools
[05:05:02] Found samtools - /usr/local/bin/samtools
[05:05:02] Found java - /usr/local/bin/java
[05:05:02] Found snpEff - /usr/local/bin/snpEff
[05:05:02] Found samclip - /usr/local/bin/samclip
[05:05:02] Found seqtk - /usr/local/bin/seqtk
[05:05:02] Found parallel - /usr/local/bin/parallel
[05:05:02] Found freebayes - /usr/local/bin/freebayes
[05:05:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:02] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:02] Found gzip - /bin/gzip
[05:05:02] Found vt - /usr/local/bin/vt
[05:05:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:05:36] This is snippy 4.6.0Show full stderr[05:05:36] This is snippy 4.6.0
[05:05:36] Written by Torsten Seemann
[05:05:36] Obtained from https://github.com/tseemann/snippy
[05:05:36] Detected operating system: linux
[05:05:36] Enabling bundled linux tools.
[05:05:36] Found bwa - /usr/local/bin/bwa
[05:05:36] Found bcftools - /usr/local/bin/bcftools
[05:05:36] Found samtools - /usr/local/bin/samtools
[05:05:36] Found java - /usr/local/bin/java
[05:05:36] Found snpEff - /usr/local/bin/snpEff
[05:05:36] Found samclip - /usr/local/bin/samclip
[05:05:36] Found seqtk - /usr/local/bin/seqtk
[05:05:36] Found parallel - /usr/local/bin/parallel
[05:05:36] Found freebayes - /usr/local/bin/freebayes
[05:05:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:36] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:36] Found gzip - /bin/gzip
[05:05:36] Found vt - /usr/local/bin/vt
[05:05:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:05:51] This is snippy 4.6.0Show full stderr[05:05:51] This is snippy 4.6.0
[05:05:51] Written by Torsten Seemann
[05:05:51] Obtained from https://github.com/tseemann/snippy
[05:05:51] Detected operating system: linux
[05:05:51] Enabling bundled linux tools.
[05:05:51] Found bwa - /usr/local/bin/bwa
[05:05:51] Found bcftools - /usr/local/bin/bcftools
[05:05:51] Found samtools - /usr/local/bin/samtools
[05:05:51] Found java - /usr/local/bin/java
[05:05:51] Found snpEff - /usr/local/bin/snpEff
[05:05:51] Found samclip - /usr/local/bin/samclip
[05:05:51] Found seqtk - /usr/local/bin/seqtk
[05:05:51] Found parallel - /usr/local/bin/parallel
[05:05:51] Found freebayes - /usr/local/bin/freebayes
[05:05:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:51] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:51] Found gzip - /bin/gzip
[05:05:51] Found vt - /usr/local/bin/vt
[05:05:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:06:06] This is snippy 4.6.0Show full stderr[05:06:06] This is snippy 4.6.0
[05:06:06] Written by Torsten Seemann
[05:06:06] Obtained from https://github.com/tseemann/snippy
[05:06:06] Detected operating system: linux
[05:06:06] Enabling bundled linux tools.
[05:06:06] Found bwa - /usr/local/bin/bwa
[05:06:06] Found bcftools - /usr/local/bin/bcftools
[05:06:06] Found samtools - /usr/local/bin/samtools
[05:06:06] Found java - /usr/local/bin/java
[05:06:06] Found snpEff - /usr/local/bin/snpEff
[05:06:06] Found samclip - /usr/local/bin/samclip
[05:06:06] Found seqtk - /usr/local/bin/seqtk
[05:06:06] Found parallel - /usr/local/bin/parallel
[05:06:06] Found freebayes - /usr/local/bin/freebayes
[05:06:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:06:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:06:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:06:06] Found vcfuniq - /usr/local/bin/vcfuniq
[05:06:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:06:06] Found gzip - /bin/gzip
[05:06:06] Found vt - /usr/local/bin/vt
[05:06:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:06:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:06:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:06:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:06:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:06:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:06:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:06:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:03:47] This is snippy 4.6.0Show full stderr[05:03:47] This is snippy 4.6.0
[05:03:47] Written by Torsten Seemann
[05:03:47] Obtained from https://github.com/tseemann/snippy
[05:03:47] Detected operating system: linux
[05:03:47] Enabling bundled linux tools.
[05:03:47] Found bwa - /usr/local/bin/bwa
[05:03:47] Found bcftools - /usr/local/bin/bcftools
[05:03:47] Found samtools - /usr/local/bin/samtools
[05:03:47] Found java - /usr/local/bin/java
[05:03:47] Found snpEff - /usr/local/bin/snpEff
[05:03:47] Found samclip - /usr/local/bin/samclip
[05:03:47] Found seqtk - /usr/local/bin/seqtk
[05:03:47] Found parallel - /usr/local/bin/parallel
[05:03:47] Found freebayes - /usr/local/bin/freebayes
[05:03:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:47] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:47] Found gzip - /bin/gzip
[05:03:47] Found vt - /usr/local/bin/vt
[05:03:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:07:09] This is snippy 4.6.0Show full stderr[05:07:09] This is snippy 4.6.0
[05:07:09] Written by Torsten Seemann
[05:07:09] Obtained from https://github.com/tseemann/snippy
[05:07:09] Detected operating system: linux
[05:07:09] Enabling bundled linux tools.
[05:07:09] Found bwa - /usr/local/bin/bwa
[05:07:09] Found bcftools - /usr/local/bin/bcftools
[05:07:09] Found samtools - /usr/local/bin/samtools
[05:07:09] Found java - /usr/local/bin/java
[05:07:09] Found snpEff - /usr/local/bin/snpEff
[05:07:09] Found samclip - /usr/local/bin/samclip
[05:07:09] Found seqtk - /usr/local/bin/seqtk
[05:07:09] Found parallel - /usr/local/bin/parallel
[05:07:09] Found freebayes - /usr/local/bin/freebayes
[05:07:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:09] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:09] Found gzip - /bin/gzip
[05:07:09] Found vt - /usr/local/bin/vt
[05:07:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:10:42] This is snippy 4.6.0Show full stderr[05:10:42] This is snippy 4.6.0
[05:10:42] Written by Torsten Seemann
[05:10:42] Obtained from https://github.com/tseemann/snippy
[05:10:42] Detected operating system: linux
[05:10:42] Enabling bundled linux tools.
[05:10:42] Found bwa - /usr/local/bin/bwa
[05:10:42] Found bcftools - /usr/local/bin/bcftools
[05:10:42] Found samtools - /usr/local/bin/samtools
[05:10:42] Found java - /usr/local/bin/java
[05:10:42] Found snpEff - /usr/local/bin/snpEff
[05:10:42] Found samclip - /usr/local/bin/samclip
[05:10:43] Found seqtk - /usr/local/bin/seqtk
[05:10:43] Found parallel - /usr/local/bin/parallel
[05:10:43] Found freebayes - /usr/local/bin/freebayes
[05:10:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:43] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:43] Found gzip - /bin/gzip
[05:10:43] Found vt - /usr/local/bin/vt
[05:10:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:10:54] This is snippy 4.6.0Show full stderr[05:10:54] This is snippy 4.6.0
[05:10:54] Written by Torsten Seemann
[05:10:54] Obtained from https://github.com/tseemann/snippy
[05:10:54] Detected operating system: linux
[05:10:54] Enabling bundled linux tools.
[05:10:54] Found bwa - /usr/local/bin/bwa
[05:10:54] Found bcftools - /usr/local/bin/bcftools
[05:10:54] Found samtools - /usr/local/bin/samtools
[05:10:54] Found java - /usr/local/bin/java
[05:10:54] Found snpEff - /usr/local/bin/snpEff
[05:10:54] Found samclip - /usr/local/bin/samclip
[05:10:54] Found seqtk - /usr/local/bin/seqtk
[05:10:54] Found parallel - /usr/local/bin/parallel
[05:10:54] Found freebayes - /usr/local/bin/freebayes
[05:10:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:54] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:54] Found gzip - /bin/gzip
[05:10:54] Found vt - /usr/local/bin/vt
[05:10:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:08:24] This is snippy 4.6.0Show full stderr[05:08:24] This is snippy 4.6.0
[05:08:24] Written by Torsten Seemann
[05:08:24] Obtained from https://github.com/tseemann/snippy
[05:08:24] Detected operating system: linux
[05:08:24] Enabling bundled linux tools.
[05:08:24] Found bwa - /usr/local/bin/bwa
[05:08:24] Found bcftools - /usr/local/bin/bcftools
[05:08:24] Found samtools - /usr/local/bin/samtools
[05:08:24] Found java - /usr/local/bin/java
[05:08:24] Found snpEff - /usr/local/bin/snpEff
[05:08:24] Found samclip - /usr/local/bin/samclip
[05:08:24] Found seqtk - /usr/local/bin/seqtk
[05:08:24] Found parallel - /usr/local/bin/parallel
[05:08:24] Found freebayes - /usr/local/bin/freebayes
[05:08:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:24] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:24] Found gzip - /bin/gzip
[05:08:24] Found vt - /usr/local/bin/vt
[05:08:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:09:15] This is snippy 4.6.0Show full stderr[05:09:15] This is snippy 4.6.0
[05:09:15] Written by Torsten Seemann
[05:09:15] Obtained from https://github.com/tseemann/snippy
[05:09:15] Detected operating system: linux
[05:09:15] Enabling bundled linux tools.
[05:09:15] Found bwa - /usr/local/bin/bwa
[05:09:15] Found bcftools - /usr/local/bin/bcftools
[05:09:15] Found samtools - /usr/local/bin/samtools
[05:09:15] Found java - /usr/local/bin/java
[05:09:15] Found snpEff - /usr/local/bin/snpEff
[05:09:15] Found samclip - /usr/local/bin/samclip
[05:09:15] Found seqtk - /usr/local/bin/seqtk
[05:09:15] Found parallel - /usr/local/bin/parallel
[05:09:15] Found freebayes - /usr/local/bin/freebayes
[05:09:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:15] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:15] Found gzip - /bin/gzip
[05:09:15] Found vt - /usr/local/bin/vt
[05:09:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:09:30] This is snippy 4.6.0Show full stderr[05:09:30] This is snippy 4.6.0
[05:09:30] Written by Torsten Seemann
[05:09:30] Obtained from https://github.com/tseemann/snippy
[05:09:30] Detected operating system: linux
[05:09:30] Enabling bundled linux tools.
[05:09:30] Found bwa - /usr/local/bin/bwa
[05:09:30] Found bcftools - /usr/local/bin/bcftools
[05:09:30] Found samtools - /usr/local/bin/samtools
[05:09:30] Found java - /usr/local/bin/java
[05:09:30] Found snpEff - /usr/local/bin/snpEff
[05:09:30] Found samclip - /usr/local/bin/samclip
[05:09:30] Found seqtk - /usr/local/bin/seqtk
[05:09:30] Found parallel - /usr/local/bin/parallel
[05:09:30] Found freebayes - /usr/local/bin/freebayes
[05:09:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:30] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:30] Found gzip - /bin/gzip
[05:09:30] Found vt - /usr/local/bin/vt
[05:09:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:11:09] This is snippy 4.6.0Show full stderr[05:11:09] This is snippy 4.6.0
[05:11:09] Written by Torsten Seemann
[05:11:09] Obtained from https://github.com/tseemann/snippy
[05:11:09] Detected operating system: linux
[05:11:09] Enabling bundled linux tools.
[05:11:09] Found bwa - /usr/local/bin/bwa
[05:11:09] Found bcftools - /usr/local/bin/bcftools
[05:11:09] Found samtools - /usr/local/bin/samtools
[05:11:09] Found java - /usr/local/bin/java
[05:11:10] Found snpEff - /usr/local/bin/snpEff
[05:11:10] Found samclip - /usr/local/bin/samclip
[05:11:10] Found seqtk - /usr/local/bin/seqtk
[05:11:10] Found parallel - /usr/local/bin/parallel
[05:11:10] Found freebayes - /usr/local/bin/freebayes
[05:11:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:11:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:11:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:11:10] Found vcfuniq - /usr/local/bin/vcfuniq
[05:11:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:11:10] Found gzip - /bin/gzip
[05:11:10] Found vt - /usr/local/bin/vt
[05:11:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:11:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:11:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:11:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:11:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:11:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:11:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:11:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:11:27] This is snippy 4.6.0Show full stderr[05:11:27] This is snippy 4.6.0
[05:11:27] Written by Torsten Seemann
[05:11:27] Obtained from https://github.com/tseemann/snippy
[05:11:27] Detected operating system: linux
[05:11:27] Enabling bundled linux tools.
[05:11:27] Found bwa - /usr/local/bin/bwa
[05:11:27] Found bcftools - /usr/local/bin/bcftools
[05:11:27] Found samtools - /usr/local/bin/samtools
[05:11:27] Found java - /usr/local/bin/java
[05:11:27] Found snpEff - /usr/local/bin/snpEff
[05:11:27] Found samclip - /usr/local/bin/samclip
[05:11:27] Found seqtk - /usr/local/bin/seqtk
[05:11:27] Found parallel - /usr/local/bin/parallel
[05:11:27] Found freebayes - /usr/local/bin/freebayes
[05:11:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:11:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:11:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:11:27] Found vcfuniq - /usr/local/bin/vcfuniq
[05:11:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:11:27] Found gzip - /bin/gzip
[05:11:27] Found vt - /usr/local/bin/vt
[05:11:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:11:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:11:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:11:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:11:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:11:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:11:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:11:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [03:40:28] This is snippy 4.6.0Show full stderr[03:40:28] This is snippy 4.6.0
[03:40:28] Written by Torsten Seemann
[03:40:28] Obtained from https://github.com/tseemann/snippy
[03:40:28] Detected operating system: linux
[03:40:28] Enabling bundled linux tools.
[03:40:28] Found bwa - /usr/local/bin/bwa
[03:40:28] Found bcftools - /usr/local/bin/bcftools
[03:40:28] Found samtools - /usr/local/bin/samtools
[03:40:28] Found java - /usr/local/bin/java
[03:40:28] Found snpEff - /usr/local/bin/snpEff
[03:40:28] Found samclip - /usr/local/bin/samclip
[03:40:28] Found seqtk - /usr/local/bin/seqtk
[03:40:28] Found parallel - /usr/local/bin/parallel
[03:40:28] Found freebayes - /usr/local/bin/freebayes
[03:40:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:28] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:28] Found gzip - /bin/gzip
[03:40:28] Found vt - /usr/local/bin/vt
[03:40:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [03:40:43] This is snippy 4.6.0Show full stderr[03:40:43] This is snippy 4.6.0
[03:40:43] Written by Torsten Seemann
[03:40:43] Obtained from https://github.com/tseemann/snippy
[03:40:43] Detected operating system: linux
[03:40:43] Enabling bundled linux tools.
[03:40:43] Found bwa - /usr/local/bin/bwa
[03:40:43] Found bcftools - /usr/local/bin/bcftools
[03:40:43] Found samtools - /usr/local/bin/samtools
[03:40:43] Found java - /usr/local/bin/java
[03:40:43] Found snpEff - /usr/local/bin/snpEff
[03:40:43] Found samclip - /usr/local/bin/samclip
[03:40:43] Found seqtk - /usr/local/bin/seqtk
[03:40:43] Found parallel - /usr/local/bin/parallel
[03:40:43] Found freebayes - /usr/local/bin/freebayes
[03:40:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:43] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:43] Found gzip - /bin/gzip
[03:40:43] Found vt - /usr/local/bin/vt
[03:40:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [03:41:14] This is snippy 4.6.0Show full stderr[03:41:14] This is snippy 4.6.0
[03:41:14] Written by Torsten Seemann
[03:41:14] Obtained from https://github.com/tseemann/snippy
[03:41:14] Detected operating system: linux
[03:41:14] Enabling bundled linux tools.
[03:41:14] Found bwa - /usr/local/bin/bwa
[03:41:14] Found bcftools - /usr/local/bin/bcftools
[03:41:14] Found samtools - /usr/local/bin/samtools
[03:41:14] Found java - /usr/local/bin/java
[03:41:14] Found snpEff - /usr/local/bin/snpEff
[03:41:14] Found samclip - /usr/local/bin/samclip
[03:41:14] Found seqtk - /usr/local/bin/seqtk
[03:41:14] Found parallel - /usr/local/bin/parallel
[03:41:14] Found freebayes - /usr/local/bin/freebayes
[03:41:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:41:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:41:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:41:14] Found vcfuniq - /usr/local/bin/vcfuniq
[03:41:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:41:14] Found gzip - /bin/gzip
[03:41:14] Found vt - /usr/local/bin/vt
[03:41:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:41:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:41:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:41:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:41:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:41:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:41:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:41:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [03:41:07] This is snippy 4.6.0Show full stderr[03:41:07] This is snippy 4.6.0
[03:41:07] Written by Torsten Seemann
[03:41:07] Obtained from https://github.com/tseemann/snippy
[03:41:07] Detected operating system: linux
[03:41:07] Enabling bundled linux tools.
[03:41:07] Found bwa - /usr/local/bin/bwa
[03:41:07] Found bcftools - /usr/local/bin/bcftools
[03:41:07] Found samtools - /usr/local/bin/samtools
[03:41:07] Found java - /usr/local/bin/java
[03:41:07] Found snpEff - /usr/local/bin/snpEff
[03:41:07] Found samclip - /usr/local/bin/samclip
[03:41:07] Found seqtk - /usr/local/bin/seqtk
[03:41:07] Found parallel - /usr/local/bin/parallel
[03:41:07] Found freebayes - /usr/local/bin/freebayes
[03:41:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:41:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:41:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:41:07] Found vcfuniq - /usr/local/bin/vcfuniq
[03:41:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:41:07] Found gzip - /bin/gzip
[03:41:07] Found vt - /usr/local/bin/vt
[03:41:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:41:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:41:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:41:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:41:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:41:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:41:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:41:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [03:41:24] This is snippy 4.6.0Show full stderr[03:41:24] This is snippy 4.6.0
[03:41:24] Written by Torsten Seemann
[03:41:24] Obtained from https://github.com/tseemann/snippy
[03:41:24] Detected operating system: linux
[03:41:24] Enabling bundled linux tools.
[03:41:24] Found bwa - /usr/local/bin/bwa
[03:41:24] Found bcftools - /usr/local/bin/bcftools
[03:41:24] Found samtools - /usr/local/bin/samtools
[03:41:24] Found java - /usr/local/bin/java
[03:41:24] Found snpEff - /usr/local/bin/snpEff
[03:41:24] Found samclip - /usr/local/bin/samclip
[03:41:24] Found seqtk - /usr/local/bin/seqtk
[03:41:24] Found parallel - /usr/local/bin/parallel
[03:41:24] Found freebayes - /usr/local/bin/freebayes
[03:41:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:41:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:41:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:41:24] Found vcfuniq - /usr/local/bin/vcfuniq
[03:41:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:41:24] Found gzip - /bin/gzip
[03:41:24] Found vt - /usr/local/bin/vt
[03:41:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:41:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:41:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:41:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:41:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:41:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:41:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:41:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [03:40:13] This is snippy 4.6.0Show full stderr[03:40:13] This is snippy 4.6.0
[03:40:13] Written by Torsten Seemann
[03:40:13] Obtained from https://github.com/tseemann/snippy
[03:40:13] Detected operating system: linux
[03:40:13] Enabling bundled linux tools.
[03:40:13] Found bwa - /usr/local/bin/bwa
[03:40:13] Found bcftools - /usr/local/bin/bcftools
[03:40:13] Found samtools - /usr/local/bin/samtools
[03:40:13] Found java - /usr/local/bin/java
[03:40:13] Found snpEff - /usr/local/bin/snpEff
[03:40:13] Found samclip - /usr/local/bin/samclip
[03:40:13] Found seqtk - /usr/local/bin/seqtk
[03:40:13] Found parallel - /usr/local/bin/parallel
[03:40:13] Found freebayes - /usr/local/bin/freebayes
[03:40:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:13] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:13] Found gzip - /bin/gzip
[03:40:13] Found vt - /usr/local/bin/vt
[03:40:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:58:25] This is snippy 4.6.0Show full stderr[05:58:25] This is snippy 4.6.0
[05:58:25] Written by Torsten Seemann
[05:58:25] Obtained from https://github.com/tseemann/snippy
[05:58:25] Detected operating system: linux
[05:58:25] Enabling bundled linux tools.
[05:58:25] Found bwa - /usr/local/bin/bwa
[05:58:25] Found bcftools - /usr/local/bin/bcftools
[05:58:25] Found samtools - /usr/local/bin/samtools
[05:58:25] Found java - /usr/local/bin/java
[05:58:25] Found snpEff - /usr/local/bin/snpEff
[05:58:25] Found samclip - /usr/local/bin/samclip
[05:58:26] Found seqtk - /usr/local/bin/seqtk
[05:58:26] Found parallel - /usr/local/bin/parallel
[05:58:26] Found freebayes - /usr/local/bin/freebayes
[05:58:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:58:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:58:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:58:26] Found vcfuniq - /usr/local/bin/vcfuniq
[05:58:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:58:26] Found gzip - /bin/gzip
[05:58:26] Found vt - /usr/local/bin/vt
[05:58:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:58:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:58:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:58:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:58:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:58:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:58:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:58:27] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:58:27] Treating reference as 'fasta' format.
[05:58:27] Will use 1 CPU cores.
[05:58:27] Using read file: /corral4/main/objects/1/9/a/dataset_19a2fd78-e44a-4c3a-9cb2-f1bf03568361.dat
[05:58:27] Creating folder: Resistance_67_fasta
[05:58:27] Changing working directory: Resistance_67_fasta
[05:58:27] Creating reference folder: reference
[05:58:27] Extracting FASTA and GFF from reference.
[05:58:27] Wrote 3 sequences to ref.fa
[05:58:27] Wrote 0 features to ref.gff
[05:58:27] Shredding /corral4/main/objects/1/9/a/dataset_19a2fd78-e44a-4c3a-9cb2-f1bf03568361.dat into pseudo-reads
[05:58:31] Wrote 404330 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:58:31] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:58:31] Using BAM RG (Read Group) ID: Resistance_67_fasta
[05:58:31] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:58:31] Running: bwa index reference/ref.fa 2>> snps.log
[05:58:37] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[05:58:37] Running: ln -sf reference/ref.fa . 2>> snps.log
[05:58:37] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[05:58:37] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[05:58:37] Running: bwa mem -Y -M -R '@RG\tID:Resistance_67_fasta\tSM:Resistance_67_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/258/72258620/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/258/72258620/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/258/72258620/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
|
| 3 | [05:59:37] This is snippy 4.6.0Show full stderr[05:59:37] This is snippy 4.6.0
[05:59:37] Written by Torsten Seemann
[05:59:37] Obtained from https://github.com/tseemann/snippy
[05:59:37] Detected operating system: linux
[05:59:37] Enabling bundled linux tools.
[05:59:37] Found bwa - /usr/local/bin/bwa
[05:59:37] Found bcftools - /usr/local/bin/bcftools
[05:59:37] Found samtools - /usr/local/bin/samtools
[05:59:37] Found java - /usr/local/bin/java
[05:59:37] Found snpEff - /usr/local/bin/snpEff
[05:59:37] Found samclip - /usr/local/bin/samclip
[05:59:37] Found seqtk - /usr/local/bin/seqtk
[05:59:37] Found parallel - /usr/local/bin/parallel
[05:59:37] Found freebayes - /usr/local/bin/freebayes
[05:59:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:59:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:59:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:59:37] Found vcfuniq - /usr/local/bin/vcfuniq
[05:59:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:59:37] Found gzip - /bin/gzip
[05:59:37] Found vt - /usr/local/bin/vt
[05:59:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:59:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:59:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:59:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:59:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:59:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:59:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:59:38] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:59:38] Treating reference as 'fasta' format.
[05:59:38] Will use 1 CPU cores.
[05:59:38] Using read file: /corral4/main/objects/2/d/4/dataset_2d4b0322-be49-468a-8c39-1a7e461cee61.dat
[05:59:38] Creating folder: Resistance_78_fasta
[05:59:38] Changing working directory: Resistance_78_fasta
[05:59:38] Creating reference folder: reference
[05:59:38] Extracting FASTA and GFF from reference.
[05:59:39] Wrote 3 sequences to ref.fa
[05:59:39] Wrote 0 features to ref.gff
[05:59:39] Shredding /corral4/main/objects/2/d/4/dataset_2d4b0322-be49-468a-8c39-1a7e461cee61.dat into pseudo-reads
[05:59:40] Wrote 423200 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:59:40] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[05:59:40] Using BAM RG (Read Group) ID: Resistance_78_fasta
[05:59:40] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:59:40] Error running command, check Resistance_78_fasta/snps.log |
| 3 | [05:57:50] This is snippy 4.6.0Show full stderr[05:57:50] This is snippy 4.6.0
[05:57:50] Written by Torsten Seemann
[05:57:50] Obtained from https://github.com/tseemann/snippy
[05:57:50] Detected operating system: linux
[05:57:50] Enabling bundled linux tools.
[05:57:50] Found bwa - /usr/local/bin/bwa
[05:57:50] Found bcftools - /usr/local/bin/bcftools
[05:57:50] Found samtools - /usr/local/bin/samtools
[05:57:50] Found java - /usr/local/bin/java
[05:57:50] Found snpEff - /usr/local/bin/snpEff
[05:57:50] Found samclip - /usr/local/bin/samclip
[05:57:50] Found seqtk - /usr/local/bin/seqtk
[05:57:50] Found parallel - /usr/local/bin/parallel
[05:57:50] Found freebayes - /usr/local/bin/freebayes
[05:57:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:57:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:57:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:57:50] Found vcfuniq - /usr/local/bin/vcfuniq
[05:57:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:57:50] Found gzip - /bin/gzip
[05:57:50] Found vt - /usr/local/bin/vt
[05:57:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:57:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:57:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:57:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:57:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:57:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:57:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:57:51] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:57:51] Treating reference as 'fasta' format.
[05:57:51] Will use 1 CPU cores.
[05:57:51] Using read file: /corral4/main/objects/e/9/1/dataset_e91bfa5f-8990-48f6-be27-b003cd51f67b.dat
[05:57:51] Creating folder: Resistance_91_fasta
[05:57:51] Changing working directory: Resistance_91_fasta
[05:57:51] Creating reference folder: reference
[05:57:51] Extracting FASTA and GFF from reference.
[05:57:51] Wrote 3 sequences to ref.fa
[05:57:51] Wrote 0 features to ref.gff
[05:57:51] Shredding /corral4/main/objects/e/9/1/dataset_e91bfa5f-8990-48f6-be27-b003cd51f67b.dat into pseudo-reads
[05:57:56] Wrote 408646 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:57:56] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:57:56] Using BAM RG (Read Group) ID: Resistance_91_fasta
[05:57:56] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:57:56] Running: bwa index reference/ref.fa 2>> snps.log
[05:58:01] Error running command, check Resistance_91_fasta/snps.log |
| 3 | [06:00:38] This is snippy 4.6.0Show full stderr[06:00:38] This is snippy 4.6.0
[06:00:38] Written by Torsten Seemann
[06:00:38] Obtained from https://github.com/tseemann/snippy
[06:00:38] Detected operating system: linux
[06:00:38] Enabling bundled linux tools.
[06:00:38] Found bwa - /usr/local/bin/bwa
[06:00:38] Found bcftools - /usr/local/bin/bcftools
[06:00:38] Found samtools - /usr/local/bin/samtools
[06:00:38] Found java - /usr/local/bin/java
[06:00:38] Found snpEff - /usr/local/bin/snpEff
[06:00:38] Found samclip - /usr/local/bin/samclip
[06:00:38] Found seqtk - /usr/local/bin/seqtk
[06:00:38] Found parallel - /usr/local/bin/parallel
[06:00:38] Found freebayes - /usr/local/bin/freebayes
[06:00:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:00:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:00:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:00:38] Found vcfuniq - /usr/local/bin/vcfuniq
[06:00:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:00:38] Found gzip - /bin/gzip
[06:00:38] Found vt - /usr/local/bin/vt
[06:00:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:00:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:00:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:00:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:00:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:00:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:00:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:00:39] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[06:00:39] Treating reference as 'fasta' format.
[06:00:39] Will use 1 CPU cores.
[06:00:39] Using read file: /corral4/main/objects/6/2/a/dataset_62a43897-e30a-4af9-a292-edd238d278b3.dat
[06:00:39] Creating folder: GCF_905183075_1_MAF65v1_genomic_fna
[06:00:39] Changing working directory: GCF_905183075_1_MAF65v1_genomic_fna
[06:00:39] Creating reference folder: reference
[06:00:39] Extracting FASTA and GFF from reference.
[06:00:40] Wrote 1 sequences to ref.fa
[06:00:40] Wrote 0 features to ref.gff
[06:00:40] Shredding /corral4/main/objects/6/2/a/dataset_62a43897-e30a-4af9-a292-edd238d278b3.dat into pseudo-reads
[06:00:43] Wrote 350040 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[06:00:43] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[06:00:43] Using BAM RG (Read Group) ID: GCF_905183075_1_MAF65v1_genomic_fna
[06:00:43] Running: samtools faidx reference/ref.fa 2>> snps.log
[06:00:44] Error running command, check GCF_905183075_1_MAF65v1_genomic_fna/snps.log |
| 3 | [07:04:40] This is snippy 4.6.0Show full stderr[07:04:40] This is snippy 4.6.0
[07:04:40] Written by Torsten Seemann
[07:04:40] Obtained from https://github.com/tseemann/snippy
[07:04:40] Detected operating system: linux
[07:04:40] Enabling bundled linux tools.
[07:04:40] Found bwa - /usr/local/bin/bwa
[07:04:40] Found bcftools - /usr/local/bin/bcftools
[07:04:40] Found samtools - /usr/local/bin/samtools
[07:04:40] Found java - /usr/local/bin/java
[07:04:40] Found snpEff - /usr/local/bin/snpEff
[07:04:40] Found samclip - /usr/local/bin/samclip
[07:04:40] Found seqtk - /usr/local/bin/seqtk
[07:04:40] Found parallel - /usr/local/bin/parallel
[07:04:40] Found freebayes - /usr/local/bin/freebayes
[07:04:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:40] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:40] Found gzip - /bin/gzip
[07:04:40] Found vt - /usr/local/bin/vt
[07:04:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:41] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:04:41] Treating reference as 'fasta' format.
[07:04:41] Will use 1 CPU cores.
[07:04:41] Using read file: /corral4/main/objects/b/9/3/dataset_b931e0c8-c97a-491e-9665-7515b51f803c.dat
[07:04:41] Creating folder: BVBRC_genome_sequence___2025_10_25T135701_613_fasta
[07:04:41] Changing working directory: BVBRC_genome_sequence___2025_10_25T135701_613_fasta
[07:04:41] Creating reference folder: reference
[07:04:41] Extracting FASTA and GFF from reference.
[07:04:41] Wrote 1 sequences to ref.fa
[07:04:41] Wrote 0 features to ref.gff
[07:04:41] Shredding /corral4/main/objects/b/9/3/dataset_b931e0c8-c97a-491e-9665-7515b51f803c.dat into pseudo-reads
[07:04:43] Wrote 219280 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:04:43] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[07:04:43] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135701_613_fasta
[07:04:43] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:04:43] Running: bwa index reference/ref.fa 2>> snps.log
[07:04:45] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[07:04:45] Running: ln -sf reference/ref.fa . 2>> snps.log
[07:04:45] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[07:04:45] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[07:04:45] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135701_613_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135701_613_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261362/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261362/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261362/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samcl |
| 3 | [07:06:19] This is snippy 4.6.0Show full stderr[07:06:19] This is snippy 4.6.0
[07:06:19] Written by Torsten Seemann
[07:06:19] Obtained from https://github.com/tseemann/snippy
[07:06:19] Detected operating system: linux
[07:06:19] Enabling bundled linux tools.
[07:06:19] Found bwa - /usr/local/bin/bwa
[07:06:19] Found bcftools - /usr/local/bin/bcftools
[07:06:19] Found samtools - /usr/local/bin/samtools
[07:06:19] Found java - /usr/local/bin/java
[07:06:19] Found snpEff - /usr/local/bin/snpEff
[07:06:19] Found samclip - /usr/local/bin/samclip
[07:06:19] Found seqtk - /usr/local/bin/seqtk
[07:06:19] Found parallel - /usr/local/bin/parallel
[07:06:19] Found freebayes - /usr/local/bin/freebayes
[07:06:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:19] Found gzip - /bin/gzip
[07:06:19] Found vt - /usr/local/bin/vt
[07:06:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:20] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:06:20] Treating reference as 'fasta' format.
[07:06:20] Will use 1 CPU cores.
[07:06:20] Using read file: /corral4/main/objects/0/6/9/dataset_06964298-cc9f-4687-8505-bd01ff7cfad2.dat
[07:06:20] Creating folder: BVBRC_genome_sequence___2025_10_25T135853_778_fasta
[07:06:20] Changing working directory: BVBRC_genome_sequence___2025_10_25T135853_778_fasta
[07:06:20] Creating reference folder: reference
[07:06:20] Extracting FASTA and GFF from reference.
[07:06:20] Wrote 1 sequences to ref.fa
[07:06:20] Wrote 0 features to ref.gff
[07:06:20] Shredding /corral4/main/objects/0/6/9/dataset_06964298-cc9f-4687-8505-bd01ff7cfad2.dat into pseudo-reads
[07:06:22] Wrote 225244 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:06:22] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[07:06:22] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135853_778_fasta
[07:06:22] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:06:23] Running: bwa index reference/ref.fa 2>> snps.log
[07:06:23] Error running command, check BVBRC_genome_sequence___2025_10_25T135853_778_fasta/snps.log |
| 3 | [06:48:27] This is snippy 4.6.0Show full stderr[06:48:27] This is snippy 4.6.0
[06:48:27] Written by Torsten Seemann
[06:48:27] Obtained from https://github.com/tseemann/snippy
[06:48:27] Detected operating system: linux
[06:48:27] Enabling bundled linux tools.
[06:48:27] Found bwa - /usr/local/bin/bwa
[06:48:27] Found bcftools - /usr/local/bin/bcftools
[06:48:27] Found samtools - /usr/local/bin/samtools
[06:48:27] Found java - /usr/local/bin/java
[06:48:27] Found snpEff - /usr/local/bin/snpEff
[06:48:27] Found samclip - /usr/local/bin/samclip
[06:48:27] Found seqtk - /usr/local/bin/seqtk
[06:48:27] Found parallel - /usr/local/bin/parallel
[06:48:27] Found freebayes - /usr/local/bin/freebayes
[06:48:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:27] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:27] Found gzip - /bin/gzip
[06:48:27] Found vt - /usr/local/bin/vt
[06:48:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:07:13] This is snippy 4.6.0Show full stderr[07:07:13] This is snippy 4.6.0
[07:07:13] Written by Torsten Seemann
[07:07:13] Obtained from https://github.com/tseemann/snippy
[07:07:13] Detected operating system: linux
[07:07:13] Enabling bundled linux tools.
[07:07:13] Found bwa - /usr/local/bin/bwa
[07:07:13] Found bcftools - /usr/local/bin/bcftools
[07:07:13] Found samtools - /usr/local/bin/samtools
[07:07:13] Found java - /usr/local/bin/java
[07:07:13] Found snpEff - /usr/local/bin/snpEff
[07:07:13] Found samclip - /usr/local/bin/samclip
[07:07:13] Found seqtk - /usr/local/bin/seqtk
[07:07:13] Found parallel - /usr/local/bin/parallel
[07:07:13] Found freebayes - /usr/local/bin/freebayes
[07:07:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:13] Found gzip - /bin/gzip
[07:07:13] Found vt - /usr/local/bin/vt
[07:07:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:48:14] This is snippy 4.6.0Show full stderr[06:48:14] This is snippy 4.6.0
[06:48:14] Written by Torsten Seemann
[06:48:14] Obtained from https://github.com/tseemann/snippy
[06:48:14] Detected operating system: linux
[06:48:14] Enabling bundled linux tools.
[06:48:14] Found bwa - /usr/local/bin/bwa
[06:48:14] Found bcftools - /usr/local/bin/bcftools
[06:48:14] Found samtools - /usr/local/bin/samtools
[06:48:14] Found java - /usr/local/bin/java
[06:48:14] Found snpEff - /usr/local/bin/snpEff
[06:48:14] Found samclip - /usr/local/bin/samclip
[06:48:14] Found seqtk - /usr/local/bin/seqtk
[06:48:14] Found parallel - /usr/local/bin/parallel
[06:48:14] Found freebayes - /usr/local/bin/freebayes
[06:48:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:14] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:14] Found gzip - /bin/gzip
[06:48:14] Found vt - /usr/local/bin/vt
[06:48:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:54:00] This is snippy 4.6.0Show full stderr[06:54:00] This is snippy 4.6.0
[06:54:00] Written by Torsten Seemann
[06:54:00] Obtained from https://github.com/tseemann/snippy
[06:54:00] Detected operating system: linux
[06:54:00] Enabling bundled linux tools.
[06:54:00] Found bwa - /usr/local/bin/bwa
[06:54:00] Found bcftools - /usr/local/bin/bcftools
[06:54:00] Found samtools - /usr/local/bin/samtools
[06:54:00] Found java - /usr/local/bin/java
[06:54:00] Found snpEff - /usr/local/bin/snpEff
[06:54:00] Found samclip - /usr/local/bin/samclip
[06:54:00] Found seqtk - /usr/local/bin/seqtk
[06:54:00] Found parallel - /usr/local/bin/parallel
[06:54:00] Found freebayes - /usr/local/bin/freebayes
[06:54:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:00] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:00] Found gzip - /bin/gzip
[06:54:00] Found vt - /usr/local/bin/vt
[06:54:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:49:48] This is snippy 4.6.0Show full stderr[06:49:48] This is snippy 4.6.0
[06:49:48] Written by Torsten Seemann
[06:49:48] Obtained from https://github.com/tseemann/snippy
[06:49:48] Detected operating system: linux
[06:49:48] Enabling bundled linux tools.
[06:49:48] Found bwa - /usr/local/bin/bwa
[06:49:48] Found bcftools - /usr/local/bin/bcftools
[06:49:48] Found samtools - /usr/local/bin/samtools
[06:49:48] Found java - /usr/local/bin/java
[06:49:48] Found snpEff - /usr/local/bin/snpEff
[06:49:48] Found samclip - /usr/local/bin/samclip
[06:49:48] Found seqtk - /usr/local/bin/seqtk
[06:49:48] Found parallel - /usr/local/bin/parallel
[06:49:48] Found freebayes - /usr/local/bin/freebayes
[06:49:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:49:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:49:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:49:48] Found vcfuniq - /usr/local/bin/vcfuniq
[06:49:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:49:48] Found gzip - /bin/gzip
[06:49:48] Found vt - /usr/local/bin/vt
[06:49:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:49:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:49:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:49:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:49:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:49:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:49:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:49:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:50:00] This is snippy 4.6.0Show full stderr[06:50:00] This is snippy 4.6.0
[06:50:00] Written by Torsten Seemann
[06:50:00] Obtained from https://github.com/tseemann/snippy
[06:50:00] Detected operating system: linux
[06:50:00] Enabling bundled linux tools.
[06:50:00] Found bwa - /usr/local/bin/bwa
[06:50:00] Found bcftools - /usr/local/bin/bcftools
[06:50:00] Found samtools - /usr/local/bin/samtools
[06:50:00] Found java - /usr/local/bin/java
[06:50:00] Found snpEff - /usr/local/bin/snpEff
[06:50:00] Found samclip - /usr/local/bin/samclip
[06:50:00] Found seqtk - /usr/local/bin/seqtk
[06:50:00] Found parallel - /usr/local/bin/parallel
[06:50:00] Found freebayes - /usr/local/bin/freebayes
[06:50:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:50:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:50:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:50:00] Found vcfuniq - /usr/local/bin/vcfuniq
[06:50:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:50:00] Found gzip - /bin/gzip
[06:50:00] Found vt - /usr/local/bin/vt
[06:50:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:50:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:50:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:50:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:50:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:50:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:50:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:50:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:31:47] This is snippy 4.6.0Show full stderr[07:31:47] This is snippy 4.6.0
[07:31:47] Written by Torsten Seemann
[07:31:47] Obtained from https://github.com/tseemann/snippy
[07:31:47] Detected operating system: linux
[07:31:47] Enabling bundled linux tools.
[07:31:47] Found bwa - /usr/local/bin/bwa
[07:31:47] Found bcftools - /usr/local/bin/bcftools
[07:31:47] Found samtools - /usr/local/bin/samtools
[07:31:47] Found java - /usr/local/bin/java
[07:31:47] Found snpEff - /usr/local/bin/snpEff
[07:31:47] Found samclip - /usr/local/bin/samclip
[07:31:47] Found seqtk - /usr/local/bin/seqtk
[07:31:47] Found parallel - /usr/local/bin/parallel
[07:31:47] Found freebayes - /usr/local/bin/freebayes
[07:31:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:31:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:31:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:31:47] Found vcfuniq - /usr/local/bin/vcfuniq
[07:31:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:31:47] Found gzip - /bin/gzip
[07:31:47] Found vt - /usr/local/bin/vt
[07:31:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:31:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:31:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:31:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:31:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:31:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:31:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:31:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:38:10] This is snippy 4.6.0Show full stderr[07:38:10] This is snippy 4.6.0
[07:38:10] Written by Torsten Seemann
[07:38:10] Obtained from https://github.com/tseemann/snippy
[07:38:10] Detected operating system: linux
[07:38:10] Enabling bundled linux tools.
[07:38:10] Found bwa - /usr/local/bin/bwa
[07:38:10] Found bcftools - /usr/local/bin/bcftools
[07:38:10] Found samtools - /usr/local/bin/samtools
[07:38:10] Found java - /usr/local/bin/java
[07:38:10] Found snpEff - /usr/local/bin/snpEff
[07:38:10] Found samclip - /usr/local/bin/samclip
[07:38:10] Found seqtk - /usr/local/bin/seqtk
[07:38:10] Found parallel - /usr/local/bin/parallel
[07:38:10] Found freebayes - /usr/local/bin/freebayes
[07:38:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:10] Found gzip - /bin/gzip
[07:38:10] Found vt - /usr/local/bin/vt
[07:38:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:50:13] This is snippy 4.6.0Show full stderr[06:50:13] This is snippy 4.6.0
[06:50:13] Written by Torsten Seemann
[06:50:13] Obtained from https://github.com/tseemann/snippy
[06:50:13] Detected operating system: linux
[06:50:13] Enabling bundled linux tools.
[06:50:13] Found bwa - /usr/local/bin/bwa
[06:50:13] Found bcftools - /usr/local/bin/bcftools
[06:50:13] Found samtools - /usr/local/bin/samtools
[06:50:13] Found java - /usr/local/bin/java
[06:50:13] Found snpEff - /usr/local/bin/snpEff
[06:50:13] Found samclip - /usr/local/bin/samclip
[06:50:13] Found seqtk - /usr/local/bin/seqtk
[06:50:13] Found parallel - /usr/local/bin/parallel
[06:50:13] Found freebayes - /usr/local/bin/freebayes
[06:50:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:50:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:50:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:50:13] Found vcfuniq - /usr/local/bin/vcfuniq
[06:50:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:50:13] Found gzip - /bin/gzip
[06:50:13] Found vt - /usr/local/bin/vt
[06:50:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:50:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:50:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:50:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:50:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:50:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:50:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:50:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:50:25] This is snippy 4.6.0Show full stderr[06:50:25] This is snippy 4.6.0
[06:50:25] Written by Torsten Seemann
[06:50:25] Obtained from https://github.com/tseemann/snippy
[06:50:25] Detected operating system: linux
[06:50:25] Enabling bundled linux tools.
[06:50:25] Found bwa - /usr/local/bin/bwa
[06:50:25] Found bcftools - /usr/local/bin/bcftools
[06:50:25] Found samtools - /usr/local/bin/samtools
[06:50:25] Found java - /usr/local/bin/java
[06:50:25] Found snpEff - /usr/local/bin/snpEff
[06:50:25] Found samclip - /usr/local/bin/samclip
[06:50:25] Found seqtk - /usr/local/bin/seqtk
[06:50:25] Found parallel - /usr/local/bin/parallel
[06:50:25] Found freebayes - /usr/local/bin/freebayes
[06:50:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:50:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:50:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:50:25] Found vcfuniq - /usr/local/bin/vcfuniq
[06:50:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:50:25] Found gzip - /bin/gzip
[06:50:25] Found vt - /usr/local/bin/vt
[06:50:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:50:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:50:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:50:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:50:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:50:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:50:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:50:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:51:40] This is snippy 4.6.0Show full stderr[06:51:40] This is snippy 4.6.0
[06:51:40] Written by Torsten Seemann
[06:51:40] Obtained from https://github.com/tseemann/snippy
[06:51:40] Detected operating system: linux
[06:51:40] Enabling bundled linux tools.
[06:51:40] Found bwa - /usr/local/bin/bwa
[06:51:40] Found bcftools - /usr/local/bin/bcftools
[06:51:40] Found samtools - /usr/local/bin/samtools
[06:51:40] Found java - /usr/local/bin/java
[06:51:40] Found snpEff - /usr/local/bin/snpEff
[06:51:40] Found samclip - /usr/local/bin/samclip
[06:51:40] Found seqtk - /usr/local/bin/seqtk
[06:51:40] Found parallel - /usr/local/bin/parallel
[06:51:40] Found freebayes - /usr/local/bin/freebayes
[06:51:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:51:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:51:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:51:40] Found vcfuniq - /usr/local/bin/vcfuniq
[06:51:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:51:40] Found gzip - /bin/gzip
[06:51:40] Found vt - /usr/local/bin/vt
[06:51:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:51:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:51:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:51:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:51:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:51:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:51:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:51:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:52:10] This is snippy 4.6.0Show full stderr[06:52:10] This is snippy 4.6.0
[06:52:10] Written by Torsten Seemann
[06:52:10] Obtained from https://github.com/tseemann/snippy
[06:52:10] Detected operating system: linux
[06:52:10] Enabling bundled linux tools.
[06:52:10] Found bwa - /usr/local/bin/bwa
[06:52:10] Found bcftools - /usr/local/bin/bcftools
[06:52:10] Found samtools - /usr/local/bin/samtools
[06:52:10] Found java - /usr/local/bin/java
[06:52:10] Found snpEff - /usr/local/bin/snpEff
[06:52:10] Found samclip - /usr/local/bin/samclip
[06:52:10] Found seqtk - /usr/local/bin/seqtk
[06:52:10] Found parallel - /usr/local/bin/parallel
[06:52:10] Found freebayes - /usr/local/bin/freebayes
[06:52:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:10] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:10] Found gzip - /bin/gzip
[06:52:10] Found vt - /usr/local/bin/vt
[06:52:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:50:38] This is snippy 4.6.0Show full stderr[06:50:38] This is snippy 4.6.0
[06:50:38] Written by Torsten Seemann
[06:50:38] Obtained from https://github.com/tseemann/snippy
[06:50:38] Detected operating system: linux
[06:50:38] Enabling bundled linux tools.
[06:50:38] Found bwa - /usr/local/bin/bwa
[06:50:38] Found bcftools - /usr/local/bin/bcftools
[06:50:38] Found samtools - /usr/local/bin/samtools
[06:50:38] Found java - /usr/local/bin/java
[06:50:38] Found snpEff - /usr/local/bin/snpEff
[06:50:38] Found samclip - /usr/local/bin/samclip
[06:50:38] Found seqtk - /usr/local/bin/seqtk
[06:50:38] Found parallel - /usr/local/bin/parallel
[06:50:38] Found freebayes - /usr/local/bin/freebayes
[06:50:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:50:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:50:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:50:38] Found vcfuniq - /usr/local/bin/vcfuniq
[06:50:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:50:38] Found gzip - /bin/gzip
[06:50:38] Found vt - /usr/local/bin/vt
[06:50:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:50:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:50:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:50:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:50:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:50:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:50:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:50:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:51:55] This is snippy 4.6.0Show full stderr[06:51:55] This is snippy 4.6.0
[06:51:55] Written by Torsten Seemann
[06:51:55] Obtained from https://github.com/tseemann/snippy
[06:51:55] Detected operating system: linux
[06:51:55] Enabling bundled linux tools.
[06:51:55] Found bwa - /usr/local/bin/bwa
[06:51:55] Found bcftools - /usr/local/bin/bcftools
[06:51:55] Found samtools - /usr/local/bin/samtools
[06:51:55] Found java - /usr/local/bin/java
[06:51:55] Found snpEff - /usr/local/bin/snpEff
[06:51:55] Found samclip - /usr/local/bin/samclip
[06:51:55] Found seqtk - /usr/local/bin/seqtk
[06:51:55] Found parallel - /usr/local/bin/parallel
[06:51:55] Found freebayes - /usr/local/bin/freebayes
[06:51:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:51:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:51:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:51:55] Found vcfuniq - /usr/local/bin/vcfuniq
[06:51:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:51:55] Found gzip - /bin/gzip
[06:51:55] Found vt - /usr/local/bin/vt
[06:51:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:51:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:51:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:51:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:51:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:51:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:51:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:51:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:54:28] This is snippy 4.6.0Show full stderr[06:54:28] This is snippy 4.6.0
[06:54:28] Written by Torsten Seemann
[06:54:28] Obtained from https://github.com/tseemann/snippy
[06:54:28] Detected operating system: linux
[06:54:28] Enabling bundled linux tools.
[06:54:28] Found bwa - /usr/local/bin/bwa
[06:54:28] Found bcftools - /usr/local/bin/bcftools
[06:54:28] Found samtools - /usr/local/bin/samtools
[06:54:28] Found java - /usr/local/bin/java
[06:54:28] Found snpEff - /usr/local/bin/snpEff
[06:54:28] Found samclip - /usr/local/bin/samclip
[06:54:28] Found seqtk - /usr/local/bin/seqtk
[06:54:28] Found parallel - /usr/local/bin/parallel
[06:54:28] Found freebayes - /usr/local/bin/freebayes
[06:54:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:28] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:28] Found gzip - /bin/gzip
[06:54:28] Found vt - /usr/local/bin/vt
[06:54:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:51:28] This is snippy 4.6.0Show full stderr[06:51:28] This is snippy 4.6.0
[06:51:28] Written by Torsten Seemann
[06:51:28] Obtained from https://github.com/tseemann/snippy
[06:51:28] Detected operating system: linux
[06:51:28] Enabling bundled linux tools.
[06:51:28] Found bwa - /usr/local/bin/bwa
[06:51:28] Found bcftools - /usr/local/bin/bcftools
[06:51:28] Found samtools - /usr/local/bin/samtools
[06:51:28] Found java - /usr/local/bin/java
[06:51:28] Found snpEff - /usr/local/bin/snpEff
[06:51:28] Found samclip - /usr/local/bin/samclip
[06:51:28] Found seqtk - /usr/local/bin/seqtk
[06:51:28] Found parallel - /usr/local/bin/parallel
[06:51:28] Found freebayes - /usr/local/bin/freebayes
[06:51:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:51:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:51:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:51:28] Found vcfuniq - /usr/local/bin/vcfuniq
[06:51:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:51:28] Found gzip - /bin/gzip
[06:51:28] Found vt - /usr/local/bin/vt
[06:51:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:51:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:51:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:51:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:51:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:51:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:51:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:51:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:54:43] This is snippy 4.6.0Show full stderr[06:54:43] This is snippy 4.6.0
[06:54:43] Written by Torsten Seemann
[06:54:43] Obtained from https://github.com/tseemann/snippy
[06:54:43] Detected operating system: linux
[06:54:43] Enabling bundled linux tools.
[06:54:43] Found bwa - /usr/local/bin/bwa
[06:54:43] Found bcftools - /usr/local/bin/bcftools
[06:54:43] Found samtools - /usr/local/bin/samtools
[06:54:43] Found java - /usr/local/bin/java
[06:54:43] Found snpEff - /usr/local/bin/snpEff
[06:54:43] Found samclip - /usr/local/bin/samclip
[06:54:43] Found seqtk - /usr/local/bin/seqtk
[06:54:43] Found parallel - /usr/local/bin/parallel
[06:54:43] Found freebayes - /usr/local/bin/freebayes
[06:54:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:43] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:43] Found gzip - /bin/gzip
[06:54:43] Found vt - /usr/local/bin/vt
[06:54:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:54:55] This is snippy 4.6.0Show full stderr[06:54:55] This is snippy 4.6.0
[06:54:55] Written by Torsten Seemann
[06:54:55] Obtained from https://github.com/tseemann/snippy
[06:54:55] Detected operating system: linux
[06:54:55] Enabling bundled linux tools.
[06:54:55] Found bwa - /usr/local/bin/bwa
[06:54:55] Found bcftools - /usr/local/bin/bcftools
[06:54:55] Found samtools - /usr/local/bin/samtools
[06:54:55] Found java - /usr/local/bin/java
[06:54:55] Found snpEff - /usr/local/bin/snpEff
[06:54:55] Found samclip - /usr/local/bin/samclip
[06:54:55] Found seqtk - /usr/local/bin/seqtk
[06:54:55] Found parallel - /usr/local/bin/parallel
[06:54:55] Found freebayes - /usr/local/bin/freebayes
[06:54:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:55] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:55] Found gzip - /bin/gzip
[06:54:55] Found vt - /usr/local/bin/vt
[06:54:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:56:27] This is snippy 4.6.0Show full stderr[06:56:27] This is snippy 4.6.0
[06:56:27] Written by Torsten Seemann
[06:56:27] Obtained from https://github.com/tseemann/snippy
[06:56:27] Detected operating system: linux
[06:56:27] Enabling bundled linux tools.
[06:56:27] Found bwa - /usr/local/bin/bwa
[06:56:27] Found bcftools - /usr/local/bin/bcftools
[06:56:27] Found samtools - /usr/local/bin/samtools
[06:56:27] Found java - /usr/local/bin/java
[06:56:27] Found snpEff - /usr/local/bin/snpEff
[06:56:27] Found samclip - /usr/local/bin/samclip
[06:56:27] Found seqtk - /usr/local/bin/seqtk
[06:56:27] Found parallel - /usr/local/bin/parallel
[06:56:27] Found freebayes - /usr/local/bin/freebayes
[06:56:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:56:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:56:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:56:27] Found vcfuniq - /usr/local/bin/vcfuniq
[06:56:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:56:27] Found gzip - /bin/gzip
[06:56:27] Found vt - /usr/local/bin/vt
[06:56:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:56:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:56:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:56:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:56:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:56:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:56:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:56:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:56:41] This is snippy 4.6.0Show full stderr[06:56:41] This is snippy 4.6.0
[06:56:41] Written by Torsten Seemann
[06:56:41] Obtained from https://github.com/tseemann/snippy
[06:56:41] Detected operating system: linux
[06:56:41] Enabling bundled linux tools.
[06:56:41] Found bwa - /usr/local/bin/bwa
[06:56:41] Found bcftools - /usr/local/bin/bcftools
[06:56:41] Found samtools - /usr/local/bin/samtools
[06:56:41] Found java - /usr/local/bin/java
[06:56:41] Found snpEff - /usr/local/bin/snpEff
[06:56:41] Found samclip - /usr/local/bin/samclip
[06:56:41] Found seqtk - /usr/local/bin/seqtk
[06:56:41] Found parallel - /usr/local/bin/parallel
[06:56:41] Found freebayes - /usr/local/bin/freebayes
[06:56:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:56:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:56:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:56:41] Found vcfuniq - /usr/local/bin/vcfuniq
[06:56:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:56:41] Found gzip - /bin/gzip
[06:56:41] Found vt - /usr/local/bin/vt
[06:56:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:56:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:56:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:56:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:56:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:56:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:56:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:56:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:57:10] This is snippy 4.6.0Show full stderr[06:57:10] This is snippy 4.6.0
[06:57:10] Written by Torsten Seemann
[06:57:10] Obtained from https://github.com/tseemann/snippy
[06:57:10] Detected operating system: linux
[06:57:10] Enabling bundled linux tools.
[06:57:10] Found bwa - /usr/local/bin/bwa
[06:57:10] Found bcftools - /usr/local/bin/bcftools
[06:57:10] Found samtools - /usr/local/bin/samtools
[06:57:10] Found java - /usr/local/bin/java
[06:57:10] Found snpEff - /usr/local/bin/snpEff
[06:57:10] Found samclip - /usr/local/bin/samclip
[06:57:10] Found seqtk - /usr/local/bin/seqtk
[06:57:10] Found parallel - /usr/local/bin/parallel
[06:57:10] Found freebayes - /usr/local/bin/freebayes
[06:57:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:57:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:57:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:57:10] Found vcfuniq - /usr/local/bin/vcfuniq
[06:57:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:57:10] Found gzip - /bin/gzip
[06:57:10] Found vt - /usr/local/bin/vt
[06:57:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:57:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:57:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:57:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:57:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:57:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:57:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:57:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:55:10] This is snippy 4.6.0Show full stderr[06:55:10] This is snippy 4.6.0
[06:55:10] Written by Torsten Seemann
[06:55:10] Obtained from https://github.com/tseemann/snippy
[06:55:10] Detected operating system: linux
[06:55:10] Enabling bundled linux tools.
[06:55:10] Found bwa - /usr/local/bin/bwa
[06:55:10] Found bcftools - /usr/local/bin/bcftools
[06:55:10] Found samtools - /usr/local/bin/samtools
[06:55:10] Found java - /usr/local/bin/java
[06:55:10] Found snpEff - /usr/local/bin/snpEff
[06:55:10] Found samclip - /usr/local/bin/samclip
[06:55:10] Found seqtk - /usr/local/bin/seqtk
[06:55:10] Found parallel - /usr/local/bin/parallel
[06:55:10] Found freebayes - /usr/local/bin/freebayes
[06:55:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:10] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:10] Found gzip - /bin/gzip
[06:55:10] Found vt - /usr/local/bin/vt
[06:55:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:59:27] This is snippy 4.6.0Show full stderr[06:59:27] This is snippy 4.6.0
[06:59:27] Written by Torsten Seemann
[06:59:27] Obtained from https://github.com/tseemann/snippy
[06:59:27] Detected operating system: linux
[06:59:27] Enabling bundled linux tools.
[06:59:27] Found bwa - /usr/local/bin/bwa
[06:59:27] Found bcftools - /usr/local/bin/bcftools
[06:59:27] Found samtools - /usr/local/bin/samtools
[06:59:28] Found java - /usr/local/bin/java
[06:59:28] Found snpEff - /usr/local/bin/snpEff
[06:59:28] Found samclip - /usr/local/bin/samclip
[06:59:28] Found seqtk - /usr/local/bin/seqtk
[06:59:28] Found parallel - /usr/local/bin/parallel
[06:59:28] Found freebayes - /usr/local/bin/freebayes
[06:59:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:28] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:28] Found gzip - /bin/gzip
[06:59:28] Found vt - /usr/local/bin/vt
[06:59:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:01:36] This is snippy 4.6.0Show full stderr[07:01:36] This is snippy 4.6.0
[07:01:36] Written by Torsten Seemann
[07:01:36] Obtained from https://github.com/tseemann/snippy
[07:01:36] Detected operating system: linux
[07:01:36] Enabling bundled linux tools.
[07:01:36] Found bwa - /usr/local/bin/bwa
[07:01:36] Found bcftools - /usr/local/bin/bcftools
[07:01:36] Found samtools - /usr/local/bin/samtools
[07:01:36] Found java - /usr/local/bin/java
[07:01:36] Found snpEff - /usr/local/bin/snpEff
[07:01:36] Found samclip - /usr/local/bin/samclip
[07:01:36] Found seqtk - /usr/local/bin/seqtk
[07:01:36] Found parallel - /usr/local/bin/parallel
[07:01:36] Found freebayes - /usr/local/bin/freebayes
[07:01:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:01:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:01:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:01:36] Found vcfuniq - /usr/local/bin/vcfuniq
[07:01:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:01:36] Found gzip - /bin/gzip
[07:01:36] Found vt - /usr/local/bin/vt
[07:01:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:01:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:01:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:01:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:01:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:01:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:01:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:01:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:01:50] This is snippy 4.6.0Show full stderr[07:01:50] This is snippy 4.6.0
[07:01:50] Written by Torsten Seemann
[07:01:50] Obtained from https://github.com/tseemann/snippy
[07:01:50] Detected operating system: linux
[07:01:50] Enabling bundled linux tools.
[07:01:50] Found bwa - /usr/local/bin/bwa
[07:01:50] Found bcftools - /usr/local/bin/bcftools
[07:01:50] Found samtools - /usr/local/bin/samtools
[07:01:50] Found java - /usr/local/bin/java
[07:01:50] Found snpEff - /usr/local/bin/snpEff
[07:01:50] Found samclip - /usr/local/bin/samclip
[07:01:50] Found seqtk - /usr/local/bin/seqtk
[07:01:50] Found parallel - /usr/local/bin/parallel
[07:01:50] Found freebayes - /usr/local/bin/freebayes
[07:01:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:01:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:01:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:01:50] Found vcfuniq - /usr/local/bin/vcfuniq
[07:01:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:01:50] Found gzip - /bin/gzip
[07:01:50] Found vt - /usr/local/bin/vt
[07:01:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:01:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:01:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:01:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:01:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:01:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:01:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:01:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:57:35] This is snippy 4.6.0Show full stderr[06:57:35] This is snippy 4.6.0
[06:57:35] Written by Torsten Seemann
[06:57:35] Obtained from https://github.com/tseemann/snippy
[06:57:35] Detected operating system: linux
[06:57:35] Enabling bundled linux tools.
[06:57:35] Found bwa - /usr/local/bin/bwa
[06:57:35] Found bcftools - /usr/local/bin/bcftools
[06:57:35] Found samtools - /usr/local/bin/samtools
[06:57:35] Found java - /usr/local/bin/java
[06:57:35] Found snpEff - /usr/local/bin/snpEff
[06:57:35] Found samclip - /usr/local/bin/samclip
[06:57:35] Found seqtk - /usr/local/bin/seqtk
[06:57:35] Found parallel - /usr/local/bin/parallel
[06:57:35] Found freebayes - /usr/local/bin/freebayes
[06:57:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:57:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:57:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:57:35] Found vcfuniq - /usr/local/bin/vcfuniq
[06:57:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:57:35] Found gzip - /bin/gzip
[06:57:35] Found vt - /usr/local/bin/vt
[06:57:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:57:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:57:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:57:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:57:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:57:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:57:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:57:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:57:50] This is snippy 4.6.0Show full stderr[06:57:50] This is snippy 4.6.0
[06:57:50] Written by Torsten Seemann
[06:57:50] Obtained from https://github.com/tseemann/snippy
[06:57:50] Detected operating system: linux
[06:57:50] Enabling bundled linux tools.
[06:57:50] Found bwa - /usr/local/bin/bwa
[06:57:50] Found bcftools - /usr/local/bin/bcftools
[06:57:50] Found samtools - /usr/local/bin/samtools
[06:57:50] Found java - /usr/local/bin/java
[06:57:50] Found snpEff - /usr/local/bin/snpEff
[06:57:50] Found samclip - /usr/local/bin/samclip
[06:57:50] Found seqtk - /usr/local/bin/seqtk
[06:57:50] Found parallel - /usr/local/bin/parallel
[06:57:50] Found freebayes - /usr/local/bin/freebayes
[06:57:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:57:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:57:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:57:50] Found vcfuniq - /usr/local/bin/vcfuniq
[06:57:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:57:50] Found gzip - /bin/gzip
[06:57:50] Found vt - /usr/local/bin/vt
[06:57:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:57:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:57:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:57:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:57:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:57:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:57:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:57:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [06:56:55] This is snippy 4.6.0Show full stderr[06:56:55] This is snippy 4.6.0
[06:56:55] Written by Torsten Seemann
[06:56:55] Obtained from https://github.com/tseemann/snippy
[06:56:55] Detected operating system: linux
[06:56:55] Enabling bundled linux tools.
[06:56:55] Found bwa - /usr/local/bin/bwa
[06:56:55] Found bcftools - /usr/local/bin/bcftools
[06:56:55] Found samtools - /usr/local/bin/samtools
[06:56:55] Found java - /usr/local/bin/java
[06:56:55] Found snpEff - /usr/local/bin/snpEff
[06:56:55] Found samclip - /usr/local/bin/samclip
[06:56:55] Found seqtk - /usr/local/bin/seqtk
[06:56:55] Found parallel - /usr/local/bin/parallel
[06:56:55] Found freebayes - /usr/local/bin/freebayes
[06:56:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:56:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:56:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:56:55] Found vcfuniq - /usr/local/bin/vcfuniq
[06:56:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:56:55] Found gzip - /bin/gzip
[06:56:55] Found vt - /usr/local/bin/vt
[06:56:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:56:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:56:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:56:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:56:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:56:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:56:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:56:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:02:04] This is snippy 4.6.0Show full stderr[07:02:04] This is snippy 4.6.0
[07:02:04] Written by Torsten Seemann
[07:02:04] Obtained from https://github.com/tseemann/snippy
[07:02:04] Detected operating system: linux
[07:02:04] Enabling bundled linux tools.
[07:02:04] Found bwa - /usr/local/bin/bwa
[07:02:04] Found bcftools - /usr/local/bin/bcftools
[07:02:04] Found samtools - /usr/local/bin/samtools
[07:02:04] Found java - /usr/local/bin/java
[07:02:04] Found snpEff - /usr/local/bin/snpEff
[07:02:04] Found samclip - /usr/local/bin/samclip
[07:02:04] Found seqtk - /usr/local/bin/seqtk
[07:02:04] Found parallel - /usr/local/bin/parallel
[07:02:04] Found freebayes - /usr/local/bin/freebayes
[07:02:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:02:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:02:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:02:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:02:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:02:04] Found gzip - /bin/gzip
[07:02:04] Found vt - /usr/local/bin/vt
[07:02:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:02:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:02:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:02:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:02:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:02:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:02:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:02:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:02:19] This is snippy 4.6.0Show full stderr[07:02:19] This is snippy 4.6.0
[07:02:19] Written by Torsten Seemann
[07:02:19] Obtained from https://github.com/tseemann/snippy
[07:02:19] Detected operating system: linux
[07:02:19] Enabling bundled linux tools.
[07:02:19] Found bwa - /usr/local/bin/bwa
[07:02:19] Found bcftools - /usr/local/bin/bcftools
[07:02:19] Found samtools - /usr/local/bin/samtools
[07:02:19] Found java - /usr/local/bin/java
[07:02:19] Found snpEff - /usr/local/bin/snpEff
[07:02:19] Found samclip - /usr/local/bin/samclip
[07:02:19] Found seqtk - /usr/local/bin/seqtk
[07:02:19] Found parallel - /usr/local/bin/parallel
[07:02:19] Found freebayes - /usr/local/bin/freebayes
[07:02:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:02:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:02:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:02:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:02:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:02:19] Found gzip - /bin/gzip
[07:02:19] Found vt - /usr/local/bin/vt
[07:02:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:02:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:02:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:02:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:02:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:02:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:02:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:02:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:05:20] This is snippy 4.6.0Show full stderr[07:05:20] This is snippy 4.6.0
[07:05:20] Written by Torsten Seemann
[07:05:20] Obtained from https://github.com/tseemann/snippy
[07:05:20] Detected operating system: linux
[07:05:20] Enabling bundled linux tools.
[07:05:20] Found bwa - /usr/local/bin/bwa
[07:05:20] Found bcftools - /usr/local/bin/bcftools
[07:05:20] Found samtools - /usr/local/bin/samtools
[07:05:20] Found java - /usr/local/bin/java
[07:05:20] Found snpEff - /usr/local/bin/snpEff
[07:05:20] Found samclip - /usr/local/bin/samclip
[07:05:20] Found seqtk - /usr/local/bin/seqtk
[07:05:20] Found parallel - /usr/local/bin/parallel
[07:05:20] Found freebayes - /usr/local/bin/freebayes
[07:05:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:20] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:20] Found gzip - /bin/gzip
[07:05:20] Found vt - /usr/local/bin/vt
[07:05:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:02:31] This is snippy 4.6.0Show full stderr[07:02:31] This is snippy 4.6.0
[07:02:31] Written by Torsten Seemann
[07:02:31] Obtained from https://github.com/tseemann/snippy
[07:02:31] Detected operating system: linux
[07:02:31] Enabling bundled linux tools.
[07:02:31] Found bwa - /usr/local/bin/bwa
[07:02:31] Found bcftools - /usr/local/bin/bcftools
[07:02:31] Found samtools - /usr/local/bin/samtools
[07:02:31] Found java - /usr/local/bin/java
[07:02:31] Found snpEff - /usr/local/bin/snpEff
[07:02:31] Found samclip - /usr/local/bin/samclip
[07:02:31] Found seqtk - /usr/local/bin/seqtk
[07:02:31] Found parallel - /usr/local/bin/parallel
[07:02:31] Found freebayes - /usr/local/bin/freebayes
[07:02:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:02:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:02:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:02:31] Found vcfuniq - /usr/local/bin/vcfuniq
[07:02:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:02:31] Found gzip - /bin/gzip
[07:02:31] Found vt - /usr/local/bin/vt
[07:02:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:02:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:02:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:02:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:02:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:02:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:02:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:02:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:15:07] This is snippy 4.6.0Show full stderr[07:15:07] This is snippy 4.6.0
[07:15:07] Written by Torsten Seemann
[07:15:07] Obtained from https://github.com/tseemann/snippy
[07:15:07] Detected operating system: linux
[07:15:07] Enabling bundled linux tools.
[07:15:07] Found bwa - /usr/local/bin/bwa
[07:15:07] Found bcftools - /usr/local/bin/bcftools
[07:15:07] Found samtools - /usr/local/bin/samtools
[07:15:07] Found java - /usr/local/bin/java
[07:15:07] Found snpEff - /usr/local/bin/snpEff
[07:15:07] Found samclip - /usr/local/bin/samclip
[07:15:07] Found seqtk - /usr/local/bin/seqtk
[07:15:07] Found parallel - /usr/local/bin/parallel
[07:15:07] Found freebayes - /usr/local/bin/freebayes
[07:15:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:15:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:15:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:15:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:15:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:15:07] Found gzip - /bin/gzip
[07:15:07] Found vt - /usr/local/bin/vt
[07:15:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:15:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:15:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:15:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:15:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:15:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:15:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:15:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:10:57] This is snippy 4.6.0Show full stderr[07:10:57] This is snippy 4.6.0
[07:10:57] Written by Torsten Seemann
[07:10:57] Obtained from https://github.com/tseemann/snippy
[07:10:57] Detected operating system: linux
[07:10:57] Enabling bundled linux tools.
[07:10:57] Found bwa - /usr/local/bin/bwa
[07:10:57] Found bcftools - /usr/local/bin/bcftools
[07:10:57] Found samtools - /usr/local/bin/samtools
[07:10:57] Found java - /usr/local/bin/java
[07:10:57] Found snpEff - /usr/local/bin/snpEff
[07:10:57] Found samclip - /usr/local/bin/samclip
[07:10:57] Found seqtk - /usr/local/bin/seqtk
[07:10:57] Found parallel - /usr/local/bin/parallel
[07:10:57] Found freebayes - /usr/local/bin/freebayes
[07:10:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:10:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:10:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:10:57] Found vcfuniq - /usr/local/bin/vcfuniq
[07:10:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:10:57] Found gzip - /bin/gzip
[07:10:57] Found vt - /usr/local/bin/vt
[07:10:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:10:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:10:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:10:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:10:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:10:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:10:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:10:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:11:10] This is snippy 4.6.0Show full stderr[07:11:10] This is snippy 4.6.0
[07:11:10] Written by Torsten Seemann
[07:11:10] Obtained from https://github.com/tseemann/snippy
[07:11:10] Detected operating system: linux
[07:11:10] Enabling bundled linux tools.
[07:11:10] Found bwa - /usr/local/bin/bwa
[07:11:10] Found bcftools - /usr/local/bin/bcftools
[07:11:10] Found samtools - /usr/local/bin/samtools
[07:11:10] Found java - /usr/local/bin/java
[07:11:10] Found snpEff - /usr/local/bin/snpEff
[07:11:10] Found samclip - /usr/local/bin/samclip
[07:11:10] Found seqtk - /usr/local/bin/seqtk
[07:11:10] Found parallel - /usr/local/bin/parallel
[07:11:10] Found freebayes - /usr/local/bin/freebayes
[07:11:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:11:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:11:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:11:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:11:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:11:10] Found gzip - /bin/gzip
[07:11:10] Found vt - /usr/local/bin/vt
[07:11:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:11:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:11:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:11:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:11:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:11:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:11:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:11:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:11:23] This is snippy 4.6.0Show full stderr[07:11:23] This is snippy 4.6.0
[07:11:23] Written by Torsten Seemann
[07:11:23] Obtained from https://github.com/tseemann/snippy
[07:11:23] Detected operating system: linux
[07:11:23] Enabling bundled linux tools.
[07:11:23] Found bwa - /usr/local/bin/bwa
[07:11:23] Found bcftools - /usr/local/bin/bcftools
[07:11:23] Found samtools - /usr/local/bin/samtools
[07:11:23] Found java - /usr/local/bin/java
[07:11:23] Found snpEff - /usr/local/bin/snpEff
[07:11:23] Found samclip - /usr/local/bin/samclip
[07:11:23] Found seqtk - /usr/local/bin/seqtk
[07:11:23] Found parallel - /usr/local/bin/parallel
[07:11:23] Found freebayes - /usr/local/bin/freebayes
[07:11:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:11:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:11:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:11:23] Found vcfuniq - /usr/local/bin/vcfuniq
[07:11:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:11:23] Found gzip - /bin/gzip
[07:11:23] Found vt - /usr/local/bin/vt
[07:11:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:11:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:11:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:11:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:11:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:11:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:11:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:11:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:14:54] This is snippy 4.6.0Show full stderr[07:14:54] This is snippy 4.6.0
[07:14:54] Written by Torsten Seemann
[07:14:54] Obtained from https://github.com/tseemann/snippy
[07:14:54] Detected operating system: linux
[07:14:54] Enabling bundled linux tools.
[07:14:54] Found bwa - /usr/local/bin/bwa
[07:14:54] Found bcftools - /usr/local/bin/bcftools
[07:14:54] Found samtools - /usr/local/bin/samtools
[07:14:54] Found java - /usr/local/bin/java
[07:14:54] Found snpEff - /usr/local/bin/snpEff
[07:14:54] Found samclip - /usr/local/bin/samclip
[07:14:54] Found seqtk - /usr/local/bin/seqtk
[07:14:54] Found parallel - /usr/local/bin/parallel
[07:14:54] Found freebayes - /usr/local/bin/freebayes
[07:14:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:14:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:14:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:14:54] Found vcfuniq - /usr/local/bin/vcfuniq
[07:14:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:14:54] Found gzip - /bin/gzip
[07:14:54] Found vt - /usr/local/bin/vt
[07:14:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:14:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:14:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:14:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:14:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:14:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:14:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:14:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:14:28] This is snippy 4.6.0Show full stderr[07:14:28] This is snippy 4.6.0
[07:14:28] Written by Torsten Seemann
[07:14:28] Obtained from https://github.com/tseemann/snippy
[07:14:28] Detected operating system: linux
[07:14:28] Enabling bundled linux tools.
[07:14:28] Found bwa - /usr/local/bin/bwa
[07:14:28] Found bcftools - /usr/local/bin/bcftools
[07:14:28] Found samtools - /usr/local/bin/samtools
[07:14:28] Found java - /usr/local/bin/java
[07:14:28] Found snpEff - /usr/local/bin/snpEff
[07:14:28] Found samclip - /usr/local/bin/samclip
[07:14:28] Found seqtk - /usr/local/bin/seqtk
[07:14:28] Found parallel - /usr/local/bin/parallel
[07:14:28] Found freebayes - /usr/local/bin/freebayes
[07:14:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:14:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:14:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:14:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:14:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:14:28] Found gzip - /bin/gzip
[07:14:28] Found vt - /usr/local/bin/vt
[07:14:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:14:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:14:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:14:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:14:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:14:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:14:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:14:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:29:34] This is snippy 4.6.0Show full stderr[07:29:34] This is snippy 4.6.0
[07:29:34] Written by Torsten Seemann
[07:29:34] Obtained from https://github.com/tseemann/snippy
[07:29:34] Detected operating system: linux
[07:29:34] Enabling bundled linux tools.
[07:29:34] Found bwa - /usr/local/bin/bwa
[07:29:34] Found bcftools - /usr/local/bin/bcftools
[07:29:34] Found samtools - /usr/local/bin/samtools
[07:29:34] Found java - /usr/local/bin/java
[07:29:34] Found snpEff - /usr/local/bin/snpEff
[07:29:34] Found samclip - /usr/local/bin/samclip
[07:29:34] Found seqtk - /usr/local/bin/seqtk
[07:29:34] Found parallel - /usr/local/bin/parallel
[07:29:34] Found freebayes - /usr/local/bin/freebayes
[07:29:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:29:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:29:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:29:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:29:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:29:34] Found gzip - /bin/gzip
[07:29:34] Found vt - /usr/local/bin/vt
[07:29:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:29:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:29:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:29:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:29:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:29:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:29:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:29:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:31:21] This is snippy 4.6.0Show full stderr[07:31:21] This is snippy 4.6.0
[07:31:21] Written by Torsten Seemann
[07:31:21] Obtained from https://github.com/tseemann/snippy
[07:31:21] Detected operating system: linux
[07:31:21] Enabling bundled linux tools.
[07:31:21] Found bwa - /usr/local/bin/bwa
[07:31:21] Found bcftools - /usr/local/bin/bcftools
[07:31:21] Found samtools - /usr/local/bin/samtools
[07:31:21] Found java - /usr/local/bin/java
[07:31:21] Found snpEff - /usr/local/bin/snpEff
[07:31:21] Found samclip - /usr/local/bin/samclip
[07:31:21] Found seqtk - /usr/local/bin/seqtk
[07:31:21] Found parallel - /usr/local/bin/parallel
[07:31:21] Found freebayes - /usr/local/bin/freebayes
[07:31:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:31:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:31:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:31:21] Found vcfuniq - /usr/local/bin/vcfuniq
[07:31:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:31:21] Found gzip - /bin/gzip
[07:31:21] Found vt - /usr/local/bin/vt
[07:31:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:31:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:31:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:31:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:31:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:31:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:31:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:31:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:32:14] This is snippy 4.6.0Show full stderr[07:32:14] This is snippy 4.6.0
[07:32:14] Written by Torsten Seemann
[07:32:14] Obtained from https://github.com/tseemann/snippy
[07:32:14] Detected operating system: linux
[07:32:14] Enabling bundled linux tools.
[07:32:14] Found bwa - /usr/local/bin/bwa
[07:32:14] Found bcftools - /usr/local/bin/bcftools
[07:32:14] Found samtools - /usr/local/bin/samtools
[07:32:14] Found java - /usr/local/bin/java
[07:32:14] Found snpEff - /usr/local/bin/snpEff
[07:32:14] Found samclip - /usr/local/bin/samclip
[07:32:14] Found seqtk - /usr/local/bin/seqtk
[07:32:14] Found parallel - /usr/local/bin/parallel
[07:32:14] Found freebayes - /usr/local/bin/freebayes
[07:32:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:14] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:14] Found gzip - /bin/gzip
[07:32:14] Found vt - /usr/local/bin/vt
[07:32:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:30:01] This is snippy 4.6.0Show full stderr[07:30:01] This is snippy 4.6.0
[07:30:01] Written by Torsten Seemann
[07:30:01] Obtained from https://github.com/tseemann/snippy
[07:30:01] Detected operating system: linux
[07:30:01] Enabling bundled linux tools.
[07:30:01] Found bwa - /usr/local/bin/bwa
[07:30:01] Found bcftools - /usr/local/bin/bcftools
[07:30:01] Found samtools - /usr/local/bin/samtools
[07:30:01] Found java - /usr/local/bin/java
[07:30:01] Found snpEff - /usr/local/bin/snpEff
[07:30:01] Found samclip - /usr/local/bin/samclip
[07:30:01] Found seqtk - /usr/local/bin/seqtk
[07:30:01] Found parallel - /usr/local/bin/parallel
[07:30:01] Found freebayes - /usr/local/bin/freebayes
[07:30:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:30:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:30:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:30:01] Found vcfuniq - /usr/local/bin/vcfuniq
[07:30:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:30:01] Found gzip - /bin/gzip
[07:30:01] Found vt - /usr/local/bin/vt
[07:30:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:30:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:30:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:30:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:30:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:30:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:30:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:30:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:32:00] This is snippy 4.6.0Show full stderr[07:32:00] This is snippy 4.6.0
[07:32:00] Written by Torsten Seemann
[07:32:00] Obtained from https://github.com/tseemann/snippy
[07:32:00] Detected operating system: linux
[07:32:00] Enabling bundled linux tools.
[07:32:00] Found bwa - /usr/local/bin/bwa
[07:32:00] Found bcftools - /usr/local/bin/bcftools
[07:32:00] Found samtools - /usr/local/bin/samtools
[07:32:00] Found java - /usr/local/bin/java
[07:32:00] Found snpEff - /usr/local/bin/snpEff
[07:32:00] Found samclip - /usr/local/bin/samclip
[07:32:00] Found seqtk - /usr/local/bin/seqtk
[07:32:00] Found parallel - /usr/local/bin/parallel
[07:32:00] Found freebayes - /usr/local/bin/freebayes
[07:32:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:00] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:00] Found gzip - /bin/gzip
[07:32:00] Found vt - /usr/local/bin/vt
[07:32:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:32:27] This is snippy 4.6.0Show full stderr[07:32:27] This is snippy 4.6.0
[07:32:27] Written by Torsten Seemann
[07:32:27] Obtained from https://github.com/tseemann/snippy
[07:32:27] Detected operating system: linux
[07:32:27] Enabling bundled linux tools.
[07:32:27] Found bwa - /usr/local/bin/bwa
[07:32:27] Found bcftools - /usr/local/bin/bcftools
[07:32:27] Found samtools - /usr/local/bin/samtools
[07:32:27] Found java - /usr/local/bin/java
[07:32:27] Found snpEff - /usr/local/bin/snpEff
[07:32:27] Found samclip - /usr/local/bin/samclip
[07:32:27] Found seqtk - /usr/local/bin/seqtk
[07:32:27] Found parallel - /usr/local/bin/parallel
[07:32:27] Found freebayes - /usr/local/bin/freebayes
[07:32:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:27] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:27] Found gzip - /bin/gzip
[07:32:27] Found vt - /usr/local/bin/vt
[07:32:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:33:07] This is snippy 4.6.0Show full stderr[07:33:07] This is snippy 4.6.0
[07:33:07] Written by Torsten Seemann
[07:33:07] Obtained from https://github.com/tseemann/snippy
[07:33:07] Detected operating system: linux
[07:33:07] Enabling bundled linux tools.
[07:33:07] Found bwa - /usr/local/bin/bwa
[07:33:07] Found bcftools - /usr/local/bin/bcftools
[07:33:07] Found samtools - /usr/local/bin/samtools
[07:33:07] Found java - /usr/local/bin/java
[07:33:07] Found snpEff - /usr/local/bin/snpEff
[07:33:07] Found samclip - /usr/local/bin/samclip
[07:33:07] Found seqtk - /usr/local/bin/seqtk
[07:33:07] Found parallel - /usr/local/bin/parallel
[07:33:07] Found freebayes - /usr/local/bin/freebayes
[07:33:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:33:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:33:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:33:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:33:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:33:07] Found gzip - /bin/gzip
[07:33:07] Found vt - /usr/local/bin/vt
[07:33:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:33:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:33:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:33:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:33:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:33:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:33:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:33:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:33:20] This is snippy 4.6.0Show full stderr[07:33:20] This is snippy 4.6.0
[07:33:20] Written by Torsten Seemann
[07:33:20] Obtained from https://github.com/tseemann/snippy
[07:33:20] Detected operating system: linux
[07:33:20] Enabling bundled linux tools.
[07:33:20] Found bwa - /usr/local/bin/bwa
[07:33:20] Found bcftools - /usr/local/bin/bcftools
[07:33:20] Found samtools - /usr/local/bin/samtools
[07:33:20] Found java - /usr/local/bin/java
[07:33:20] Found snpEff - /usr/local/bin/snpEff
[07:33:20] Found samclip - /usr/local/bin/samclip
[07:33:20] Found seqtk - /usr/local/bin/seqtk
[07:33:20] Found parallel - /usr/local/bin/parallel
[07:33:20] Found freebayes - /usr/local/bin/freebayes
[07:33:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:33:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:33:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:33:20] Found vcfuniq - /usr/local/bin/vcfuniq
[07:33:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:33:20] Found gzip - /bin/gzip
[07:33:20] Found vt - /usr/local/bin/vt
[07:33:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:33:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:33:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:33:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:33:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:33:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:33:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:33:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:33:44] This is snippy 4.6.0Show full stderr[07:33:44] This is snippy 4.6.0
[07:33:44] Written by Torsten Seemann
[07:33:44] Obtained from https://github.com/tseemann/snippy
[07:33:44] Detected operating system: linux
[07:33:44] Enabling bundled linux tools.
[07:33:44] Found bwa - /usr/local/bin/bwa
[07:33:44] Found bcftools - /usr/local/bin/bcftools
[07:33:44] Found samtools - /usr/local/bin/samtools
[07:33:44] Found java - /usr/local/bin/java
[07:33:44] Found snpEff - /usr/local/bin/snpEff
[07:33:44] Found samclip - /usr/local/bin/samclip
[07:33:44] Found seqtk - /usr/local/bin/seqtk
[07:33:44] Found parallel - /usr/local/bin/parallel
[07:33:44] Found freebayes - /usr/local/bin/freebayes
[07:33:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:33:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:33:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:33:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:33:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:33:44] Found gzip - /bin/gzip
[07:33:44] Found vt - /usr/local/bin/vt
[07:33:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:33:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:33:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:33:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:33:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:33:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:33:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:33:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:34:25] This is snippy 4.6.0Show full stderr[07:34:25] This is snippy 4.6.0
[07:34:25] Written by Torsten Seemann
[07:34:25] Obtained from https://github.com/tseemann/snippy
[07:34:25] Detected operating system: linux
[07:34:25] Enabling bundled linux tools.
[07:34:25] Found bwa - /usr/local/bin/bwa
[07:34:25] Found bcftools - /usr/local/bin/bcftools
[07:34:25] Found samtools - /usr/local/bin/samtools
[07:34:25] Found java - /usr/local/bin/java
[07:34:25] Found snpEff - /usr/local/bin/snpEff
[07:34:25] Found samclip - /usr/local/bin/samclip
[07:34:25] Found seqtk - /usr/local/bin/seqtk
[07:34:25] Found parallel - /usr/local/bin/parallel
[07:34:25] Found freebayes - /usr/local/bin/freebayes
[07:34:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:34:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:34:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:34:25] Found vcfuniq - /usr/local/bin/vcfuniq
[07:34:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:34:25] Found gzip - /bin/gzip
[07:34:25] Found vt - /usr/local/bin/vt
[07:34:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:34:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:34:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:34:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:34:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:34:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:34:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:34:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:34:52] This is snippy 4.6.0Show full stderr[07:34:52] This is snippy 4.6.0
[07:34:52] Written by Torsten Seemann
[07:34:52] Obtained from https://github.com/tseemann/snippy
[07:34:52] Detected operating system: linux
[07:34:52] Enabling bundled linux tools.
[07:34:52] Found bwa - /usr/local/bin/bwa
[07:34:52] Found bcftools - /usr/local/bin/bcftools
[07:34:52] Found samtools - /usr/local/bin/samtools
[07:34:52] Found java - /usr/local/bin/java
[07:34:52] Found snpEff - /usr/local/bin/snpEff
[07:34:52] Found samclip - /usr/local/bin/samclip
[07:34:52] Found seqtk - /usr/local/bin/seqtk
[07:34:52] Found parallel - /usr/local/bin/parallel
[07:34:52] Found freebayes - /usr/local/bin/freebayes
[07:34:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:34:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:34:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:34:52] Found vcfuniq - /usr/local/bin/vcfuniq
[07:34:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:34:52] Found gzip - /bin/gzip
[07:34:52] Found vt - /usr/local/bin/vt
[07:34:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:34:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:34:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:34:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:34:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:34:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:34:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:34:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:37:43] This is snippy 4.6.0Show full stderr[07:37:43] This is snippy 4.6.0
[07:37:43] Written by Torsten Seemann
[07:37:43] Obtained from https://github.com/tseemann/snippy
[07:37:43] Detected operating system: linux
[07:37:43] Enabling bundled linux tools.
[07:37:43] Found bwa - /usr/local/bin/bwa
[07:37:43] Found bcftools - /usr/local/bin/bcftools
[07:37:43] Found samtools - /usr/local/bin/samtools
[07:37:43] Found java - /usr/local/bin/java
[07:37:43] Found snpEff - /usr/local/bin/snpEff
[07:37:43] Found samclip - /usr/local/bin/samclip
[07:37:43] Found seqtk - /usr/local/bin/seqtk
[07:37:43] Found parallel - /usr/local/bin/parallel
[07:37:43] Found freebayes - /usr/local/bin/freebayes
[07:37:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:37:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:37:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:37:43] Found vcfuniq - /usr/local/bin/vcfuniq
[07:37:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:37:43] Found gzip - /bin/gzip
[07:37:43] Found vt - /usr/local/bin/vt
[07:37:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:37:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:37:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:37:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:37:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:37:58] This is snippy 4.6.0Show full stderr[07:37:58] This is snippy 4.6.0
[07:37:58] Written by Torsten Seemann
[07:37:58] Obtained from https://github.com/tseemann/snippy
[07:37:58] Detected operating system: linux
[07:37:58] Enabling bundled linux tools.
[07:37:58] Found bwa - /usr/local/bin/bwa
[07:37:58] Found bcftools - /usr/local/bin/bcftools
[07:37:58] Found samtools - /usr/local/bin/samtools
[07:37:58] Found java - /usr/local/bin/java
[07:37:58] Found snpEff - /usr/local/bin/snpEff
[07:37:58] Found samclip - /usr/local/bin/samclip
[07:37:58] Found seqtk - /usr/local/bin/seqtk
[07:37:58] Found parallel - /usr/local/bin/parallel
[07:37:58] Found freebayes - /usr/local/bin/freebayes
[07:37:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:37:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:37:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:37:58] Found vcfuniq - /usr/local/bin/vcfuniq
[07:37:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:37:58] Found gzip - /bin/gzip
[07:37:58] Found vt - /usr/local/bin/vt
[07:37:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:37:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:37:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:37:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:37:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:40:37] This is snippy 4.6.0Show full stderr[07:40:37] This is snippy 4.6.0
[07:40:37] Written by Torsten Seemann
[07:40:37] Obtained from https://github.com/tseemann/snippy
[07:40:37] Detected operating system: linux
[07:40:37] Enabling bundled linux tools.
[07:40:37] Found bwa - /usr/local/bin/bwa
[07:40:37] Found bcftools - /usr/local/bin/bcftools
[07:40:37] Found samtools - /usr/local/bin/samtools
[07:40:37] Found java - /usr/local/bin/java
[07:40:37] Found snpEff - /usr/local/bin/snpEff
[07:40:37] Found samclip - /usr/local/bin/samclip
[07:40:37] Found seqtk - /usr/local/bin/seqtk
[07:40:37] Found parallel - /usr/local/bin/parallel
[07:40:37] Found freebayes - /usr/local/bin/freebayes
[07:40:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:37] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:37] Found gzip - /bin/gzip
[07:40:37] Found vt - /usr/local/bin/vt
[07:40:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:41:04] This is snippy 4.6.0Show full stderr[07:41:04] This is snippy 4.6.0
[07:41:04] Written by Torsten Seemann
[07:41:04] Obtained from https://github.com/tseemann/snippy
[07:41:04] Detected operating system: linux
[07:41:04] Enabling bundled linux tools.
[07:41:04] Found bwa - /usr/local/bin/bwa
[07:41:04] Found bcftools - /usr/local/bin/bcftools
[07:41:04] Found samtools - /usr/local/bin/samtools
[07:41:04] Found java - /usr/local/bin/java
[07:41:04] Found snpEff - /usr/local/bin/snpEff
[07:41:04] Found samclip - /usr/local/bin/samclip
[07:41:04] Found seqtk - /usr/local/bin/seqtk
[07:41:04] Found parallel - /usr/local/bin/parallel
[07:41:04] Found freebayes - /usr/local/bin/freebayes
[07:41:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:41:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:41:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:41:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:41:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:41:04] Found gzip - /bin/gzip
[07:41:04] Found vt - /usr/local/bin/vt
[07:41:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:41:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:41:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:41:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:41:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:41:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:41:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:41:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:44:16] This is snippy 4.6.0Show full stderr[07:44:16] This is snippy 4.6.0
[07:44:16] Written by Torsten Seemann
[07:44:16] Obtained from https://github.com/tseemann/snippy
[07:44:16] Detected operating system: linux
[07:44:16] Enabling bundled linux tools.
[07:44:16] Found bwa - /usr/local/bin/bwa
[07:44:16] Found bcftools - /usr/local/bin/bcftools
[07:44:16] Found samtools - /usr/local/bin/samtools
[07:44:16] Found java - /usr/local/bin/java
[07:44:16] Found snpEff - /usr/local/bin/snpEff
[07:44:16] Found samclip - /usr/local/bin/samclip
[07:44:16] Found seqtk - /usr/local/bin/seqtk
[07:44:16] Found parallel - /usr/local/bin/parallel
[07:44:16] Found freebayes - /usr/local/bin/freebayes
[07:44:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:16] Found gzip - /bin/gzip
[07:44:16] Found vt - /usr/local/bin/vt
[07:44:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:47:13] This is snippy 4.6.0Show full stderr[07:47:13] This is snippy 4.6.0
[07:47:13] Written by Torsten Seemann
[07:47:13] Obtained from https://github.com/tseemann/snippy
[07:47:13] Detected operating system: linux
[07:47:13] Enabling bundled linux tools.
[07:47:13] Found bwa - /usr/local/bin/bwa
[07:47:13] Found bcftools - /usr/local/bin/bcftools
[07:47:13] Found samtools - /usr/local/bin/samtools
[07:47:13] Found java - /usr/local/bin/java
[07:47:13] Found snpEff - /usr/local/bin/snpEff
[07:47:13] Found samclip - /usr/local/bin/samclip
[07:47:13] Found seqtk - /usr/local/bin/seqtk
[07:47:13] Found parallel - /usr/local/bin/parallel
[07:47:13] Found freebayes - /usr/local/bin/freebayes
[07:47:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:47:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:47:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:47:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:47:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:47:13] Found gzip - /bin/gzip
[07:47:13] Found vt - /usr/local/bin/vt
[07:47:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:47:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:47:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:47:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:47:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:47:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:47:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:47:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [07:47:28] This is snippy 4.6.0Show full stderr[07:47:28] This is snippy 4.6.0
[07:47:28] Written by Torsten Seemann
[07:47:28] Obtained from https://github.com/tseemann/snippy
[07:47:28] Detected operating system: linux
[07:47:28] Enabling bundled linux tools.
[07:47:28] Found bwa - /usr/local/bin/bwa
[07:47:28] Found bcftools - /usr/local/bin/bcftools
[07:47:28] Found samtools - /usr/local/bin/samtools
[07:47:28] Found java - /usr/local/bin/java
[07:47:28] Found snpEff - /usr/local/bin/snpEff
[07:47:28] Found samclip - /usr/local/bin/samclip
[07:47:28] Found seqtk - /usr/local/bin/seqtk
[07:47:28] Found parallel - /usr/local/bin/parallel
[07:47:28] Found freebayes - /usr/local/bin/freebayes
[07:47:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:47:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:47:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:47:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:47:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:47:28] Found gzip - /bin/gzip
[07:47:28] Found vt - /usr/local/bin/vt
[07:47:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:47:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:47:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:47:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:47:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:47:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:47:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:47:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [04:43:22] This is snippy 4.6.0Show full stderr[04:43:22] This is snippy 4.6.0
[04:43:22] Written by Torsten Seemann
[04:43:22] Obtained from https://github.com/tseemann/snippy
[04:43:22] Detected operating system: linux
[04:43:22] Enabling bundled linux tools.
[04:43:22] Found bwa - /usr/local/bin/bwa
[04:43:22] Found bcftools - /usr/local/bin/bcftools
[04:43:22] Found samtools - /usr/local/bin/samtools
[04:43:22] Found java - /usr/local/bin/java
[04:43:22] Found snpEff - /usr/local/bin/snpEff
[04:43:22] Found samclip - /usr/local/bin/samclip
[04:43:22] Found seqtk - /usr/local/bin/seqtk
[04:43:22] Found parallel - /usr/local/bin/parallel
[04:43:22] Found freebayes - /usr/local/bin/freebayes
[04:43:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:22] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:22] Found gzip - /bin/gzip
[04:43:22] Found vt - /usr/local/bin/vt
[04:43:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [12:48:43] This is snippy 4.6.0Show full stderr[12:48:43] This is snippy 4.6.0
[12:48:43] Written by Torsten Seemann
[12:48:43] Obtained from https://github.com/tseemann/snippy
[12:48:43] Detected operating system: linux
[12:48:43] Enabling bundled linux tools.
[12:48:43] Found bwa - /usr/local/bin/bwa
[12:48:43] Found bcftools - /usr/local/bin/bcftools
[12:48:43] Found samtools - /usr/local/bin/samtools
[12:48:43] Found java - /usr/local/bin/java
[12:48:43] Found snpEff - /usr/local/bin/snpEff
[12:48:43] Found samclip - /usr/local/bin/samclip
[12:48:43] Found seqtk - /usr/local/bin/seqtk
[12:48:43] Found parallel - /usr/local/bin/parallel
[12:48:43] Found freebayes - /usr/local/bin/freebayes
[12:48:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:48:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:48:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:48:43] Found vcfuniq - /usr/local/bin/vcfuniq
[12:48:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:48:43] Found gzip - /bin/gzip
[12:48:43] Found vt - /usr/local/bin/vt
[12:48:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:48:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:48:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:48:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:48:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:48:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:48:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:48:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [12:59:35] This is snippy 4.6.0Show full stderr[12:59:35] This is snippy 4.6.0
[12:59:35] Written by Torsten Seemann
[12:59:35] Obtained from https://github.com/tseemann/snippy
[12:59:35] Detected operating system: linux
[12:59:35] Enabling bundled linux tools.
[12:59:35] Found bwa - /usr/local/bin/bwa
[12:59:35] Found bcftools - /usr/local/bin/bcftools
[12:59:35] Found samtools - /usr/local/bin/samtools
[12:59:35] Found java - /usr/local/bin/java
[12:59:35] Found snpEff - /usr/local/bin/snpEff
[12:59:35] Found samclip - /usr/local/bin/samclip
[12:59:35] Found seqtk - /usr/local/bin/seqtk
[12:59:35] Found parallel - /usr/local/bin/parallel
[12:59:35] Found freebayes - /usr/local/bin/freebayes
[12:59:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:59:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:59:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:59:35] Found vcfuniq - /usr/local/bin/vcfuniq
[12:59:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:59:35] Found gzip - /bin/gzip
[12:59:35] Found vt - /usr/local/bin/vt
[12:59:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:59:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:59:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:59:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:59:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:59:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:59:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:59:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [19:40:39] This is snippy 4.6.0Show full stderr[19:40:39] This is snippy 4.6.0
[19:40:39] Written by Torsten Seemann
[19:40:39] Obtained from https://github.com/tseemann/snippy
[19:40:39] Detected operating system: linux
[19:40:39] Enabling bundled linux tools.
[19:40:39] Found bwa - /usr/local/bin/bwa
[19:40:39] Found bcftools - /usr/local/bin/bcftools
[19:40:39] Found samtools - /usr/local/bin/samtools
[19:40:39] Found java - /usr/local/bin/java
[19:40:39] Found snpEff - /usr/local/bin/snpEff
[19:40:39] Found samclip - /usr/local/bin/samclip
[19:40:39] Found seqtk - /usr/local/bin/seqtk
[19:40:39] Found parallel - /usr/local/bin/parallel
[19:40:39] Found freebayes - /usr/local/bin/freebayes
[19:40:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:39] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:39] Found gzip - /bin/gzip
[19:40:39] Found vt - /usr/local/bin/vt
[19:40:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [14:45:15] This is snippy 4.6.0Show full stderr[14:45:15] This is snippy 4.6.0
[14:45:15] Written by Torsten Seemann
[14:45:15] Obtained from https://github.com/tseemann/snippy
[14:45:15] Detected operating system: linux
[14:45:15] Enabling bundled linux tools.
[14:45:15] Found bwa - /usr/local/bin/bwa
[14:45:15] Found bcftools - /usr/local/bin/bcftools
[14:45:15] Found samtools - /usr/local/bin/samtools
[14:45:15] Found java - /usr/local/bin/java
[14:45:15] Found snpEff - /usr/local/bin/snpEff
[14:45:15] Found samclip - /usr/local/bin/samclip
[14:45:15] Found seqtk - /usr/local/bin/seqtk
[14:45:15] Found parallel - /usr/local/bin/parallel
[14:45:15] Found freebayes - /usr/local/bin/freebayes
[14:45:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:15] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:15] Found gzip - /bin/gzip
[14:45:15] Found vt - /usr/local/bin/vt
[14:45:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [14:46:45] This is snippy 4.6.0Show full stderr[14:46:45] This is snippy 4.6.0
[14:46:45] Written by Torsten Seemann
[14:46:45] Obtained from https://github.com/tseemann/snippy
[14:46:45] Detected operating system: linux
[14:46:45] Enabling bundled linux tools.
[14:46:45] Found bwa - /usr/local/bin/bwa
[14:46:45] Found bcftools - /usr/local/bin/bcftools
[14:46:45] Found samtools - /usr/local/bin/samtools
[14:46:45] Found java - /usr/local/bin/java
[14:46:45] Found snpEff - /usr/local/bin/snpEff
[14:46:45] Found samclip - /usr/local/bin/samclip
[14:46:45] Found seqtk - /usr/local/bin/seqtk
[14:46:45] Found parallel - /usr/local/bin/parallel
[14:46:45] Found freebayes - /usr/local/bin/freebayes
[14:46:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:45] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:45] Found gzip - /bin/gzip
[14:46:45] Found vt - /usr/local/bin/vt
[14:46:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [14:51:54] This is snippy 4.6.0Show full stderr[14:51:54] This is snippy 4.6.0
[14:51:54] Written by Torsten Seemann
[14:51:54] Obtained from https://github.com/tseemann/snippy
[14:51:54] Detected operating system: linux
[14:51:54] Enabling bundled linux tools.
[14:51:54] Found bwa - /usr/local/bin/bwa
[14:51:54] Found bcftools - /usr/local/bin/bcftools
[14:51:54] Found samtools - /usr/local/bin/samtools
[14:51:54] Found java - /usr/local/bin/java
[14:51:54] Found snpEff - /usr/local/bin/snpEff
[14:51:54] Found samclip - /usr/local/bin/samclip
[14:51:54] Found seqtk - /usr/local/bin/seqtk
[14:51:54] Found parallel - /usr/local/bin/parallel
[14:51:54] Found freebayes - /usr/local/bin/freebayes
[14:51:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:54] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:54] Found gzip - /bin/gzip
[14:51:54] Found vt - /usr/local/bin/vt
[14:51:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [14:46:30] This is snippy 4.6.0Show full stderr[14:46:30] This is snippy 4.6.0
[14:46:30] Written by Torsten Seemann
[14:46:30] Obtained from https://github.com/tseemann/snippy
[14:46:30] Detected operating system: linux
[14:46:30] Enabling bundled linux tools.
[14:46:30] Found bwa - /usr/local/bin/bwa
[14:46:30] Found bcftools - /usr/local/bin/bcftools
[14:46:30] Found samtools - /usr/local/bin/samtools
[14:46:30] Found java - /usr/local/bin/java
[14:46:30] Found snpEff - /usr/local/bin/snpEff
[14:46:30] Found samclip - /usr/local/bin/samclip
[14:46:30] Found seqtk - /usr/local/bin/seqtk
[14:46:30] Found parallel - /usr/local/bin/parallel
[14:46:30] Found freebayes - /usr/local/bin/freebayes
[14:46:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:30] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:30] Found gzip - /bin/gzip
[14:46:30] Found vt - /usr/local/bin/vt
[14:46:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [14:47:39] This is snippy 4.6.0Show full stderr[14:47:39] This is snippy 4.6.0
[14:47:39] Written by Torsten Seemann
[14:47:39] Obtained from https://github.com/tseemann/snippy
[14:47:39] Detected operating system: linux
[14:47:39] Enabling bundled linux tools.
[14:47:39] Found bwa - /usr/local/bin/bwa
[14:47:39] Found bcftools - /usr/local/bin/bcftools
[14:47:39] Found samtools - /usr/local/bin/samtools
[14:47:39] Found java - /usr/local/bin/java
[14:47:39] Found snpEff - /usr/local/bin/snpEff
[14:47:39] Found samclip - /usr/local/bin/samclip
[14:47:39] Found seqtk - /usr/local/bin/seqtk
[14:47:39] Found parallel - /usr/local/bin/parallel
[14:47:39] Found freebayes - /usr/local/bin/freebayes
[14:47:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:47:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:47:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:47:39] Found vcfuniq - /usr/local/bin/vcfuniq
[14:47:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:47:39] Found gzip - /bin/gzip
[14:47:39] Found vt - /usr/local/bin/vt
[14:47:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:47:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:47:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:47:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:47:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:47:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:47:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:47:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [14:52:38] This is snippy 4.6.0Show full stderr[14:52:38] This is snippy 4.6.0
[14:52:38] Written by Torsten Seemann
[14:52:38] Obtained from https://github.com/tseemann/snippy
[14:52:38] Detected operating system: linux
[14:52:38] Enabling bundled linux tools.
[14:52:38] Found bwa - /usr/local/bin/bwa
[14:52:38] Found bcftools - /usr/local/bin/bcftools
[14:52:38] Found samtools - /usr/local/bin/samtools
[14:52:38] Found java - /usr/local/bin/java
[14:52:38] Found snpEff - /usr/local/bin/snpEff
[14:52:38] Found samclip - /usr/local/bin/samclip
[14:52:38] Found seqtk - /usr/local/bin/seqtk
[14:52:38] Found parallel - /usr/local/bin/parallel
[14:52:38] Found freebayes - /usr/local/bin/freebayes
[14:52:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:52:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:52:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:52:38] Found vcfuniq - /usr/local/bin/vcfuniq
[14:52:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:52:38] Found gzip - /bin/gzip
[14:52:38] Found vt - /usr/local/bin/vt
[14:52:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:52:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:52:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:52:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:52:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:52:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:52:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:52:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [14:52:53] This is snippy 4.6.0Show full stderr[14:52:53] This is snippy 4.6.0
[14:52:53] Written by Torsten Seemann
[14:52:53] Obtained from https://github.com/tseemann/snippy
[14:52:53] Detected operating system: linux
[14:52:53] Enabling bundled linux tools.
[14:52:53] Found bwa - /usr/local/bin/bwa
[14:52:53] Found bcftools - /usr/local/bin/bcftools
[14:52:53] Found samtools - /usr/local/bin/samtools
[14:52:53] Found java - /usr/local/bin/java
[14:52:53] Found snpEff - /usr/local/bin/snpEff
[14:52:53] Found samclip - /usr/local/bin/samclip
[14:52:53] Found seqtk - /usr/local/bin/seqtk
[14:52:53] Found parallel - /usr/local/bin/parallel
[14:52:53] Found freebayes - /usr/local/bin/freebayes
[14:52:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:52:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:52:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:52:53] Found vcfuniq - /usr/local/bin/vcfuniq
[14:52:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:52:53] Found gzip - /bin/gzip
[14:52:53] Found vt - /usr/local/bin/vt
[14:52:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:52:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:52:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:52:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:52:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:52:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:52:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:52:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [17:30:18] This is snippy 4.6.0Show full stderr[17:30:18] This is snippy 4.6.0
[17:30:18] Written by Torsten Seemann
[17:30:18] Obtained from https://github.com/tseemann/snippy
[17:30:18] Detected operating system: linux
[17:30:18] Enabling bundled linux tools.
[17:30:18] Found bwa - /usr/local/bin/bwa
[17:30:18] Found bcftools - /usr/local/bin/bcftools
[17:30:18] Found samtools - /usr/local/bin/samtools
[17:30:18] Found java - /usr/local/bin/java
[17:30:18] Found snpEff - /usr/local/bin/snpEff
[17:30:18] Found samclip - /usr/local/bin/samclip
[17:30:18] Found seqtk - /usr/local/bin/seqtk
[17:30:18] Found parallel - /usr/local/bin/parallel
[17:30:18] Found freebayes - /usr/local/bin/freebayes
[17:30:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:30:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:30:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:30:19] Found vcfuniq - /usr/local/bin/vcfuniq
[17:30:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:30:19] Found gzip - /bin/gzip
[17:30:19] Found vt - /usr/local/bin/vt
[17:30:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:30:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:30:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:30:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:30:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:30:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:30:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:30:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [17:42:52] This is snippy 4.6.0Show full stderr[17:42:52] This is snippy 4.6.0
[17:42:52] Written by Torsten Seemann
[17:42:52] Obtained from https://github.com/tseemann/snippy
[17:42:52] Detected operating system: linux
[17:42:52] Enabling bundled linux tools.
[17:42:52] Found bwa - /usr/local/bin/bwa
[17:42:52] Found bcftools - /usr/local/bin/bcftools
[17:42:52] Found samtools - /usr/local/bin/samtools
[17:42:52] Found java - /usr/local/bin/java
[17:42:52] Found snpEff - /usr/local/bin/snpEff
[17:42:52] Found samclip - /usr/local/bin/samclip
[17:42:52] Found seqtk - /usr/local/bin/seqtk
[17:42:52] Found parallel - /usr/local/bin/parallel
[17:42:52] Found freebayes - /usr/local/bin/freebayes
[17:42:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:42:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:42:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:42:52] Found vcfuniq - /usr/local/bin/vcfuniq
[17:42:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:42:52] Found gzip - /bin/gzip
[17:42:52] Found vt - /usr/local/bin/vt
[17:42:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:42:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:42:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:42:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:42:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:42:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:42:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:42:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [17:36:36] This is snippy 4.6.0Show full stderr[17:36:36] This is snippy 4.6.0
[17:36:36] Written by Torsten Seemann
[17:36:36] Obtained from https://github.com/tseemann/snippy
[17:36:36] Detected operating system: linux
[17:36:36] Enabling bundled linux tools.
[17:36:36] Found bwa - /usr/local/bin/bwa
[17:36:36] Found bcftools - /usr/local/bin/bcftools
[17:36:36] Found samtools - /usr/local/bin/samtools
[17:36:36] Found java - /usr/local/bin/java
[17:36:36] Found snpEff - /usr/local/bin/snpEff
[17:36:36] Found samclip - /usr/local/bin/samclip
[17:36:36] Found seqtk - /usr/local/bin/seqtk
[17:36:36] Found parallel - /usr/local/bin/parallel
[17:36:36] Found freebayes - /usr/local/bin/freebayes
[17:36:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:36:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:36:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:36:36] Found vcfuniq - /usr/local/bin/vcfuniq
[17:36:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:36:36] Found gzip - /bin/gzip
[17:36:36] Found vt - /usr/local/bin/vt
[17:36:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:36:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:36:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:36:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:36:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:36:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:36:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:36:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [17:37:39] This is snippy 4.6.0Show full stderr[17:37:39] This is snippy 4.6.0
[17:37:39] Written by Torsten Seemann
[17:37:39] Obtained from https://github.com/tseemann/snippy
[17:37:39] Detected operating system: linux
[17:37:39] Enabling bundled linux tools.
[17:37:39] Found bwa - /usr/local/bin/bwa
[17:37:39] Found bcftools - /usr/local/bin/bcftools
[17:37:39] Found samtools - /usr/local/bin/samtools
[17:37:39] Found java - /usr/local/bin/java
[17:37:39] Found snpEff - /usr/local/bin/snpEff
[17:37:39] Found samclip - /usr/local/bin/samclip
[17:37:39] Found seqtk - /usr/local/bin/seqtk
[17:37:39] Found parallel - /usr/local/bin/parallel
[17:37:39] Found freebayes - /usr/local/bin/freebayes
[17:37:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:37:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:37:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:37:39] Found vcfuniq - /usr/local/bin/vcfuniq
[17:37:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:37:39] Found gzip - /bin/gzip
[17:37:39] Found vt - /usr/local/bin/vt
[17:37:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:37:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:37:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:37:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:37:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:37:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:37:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:37:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [17:38:19] This is snippy 4.6.0Show full stderr[17:38:19] This is snippy 4.6.0
[17:38:19] Written by Torsten Seemann
[17:38:19] Obtained from https://github.com/tseemann/snippy
[17:38:19] Detected operating system: linux
[17:38:19] Enabling bundled linux tools.
[17:38:19] Found bwa - /usr/local/bin/bwa
[17:38:19] Found bcftools - /usr/local/bin/bcftools
[17:38:19] Found samtools - /usr/local/bin/samtools
[17:38:19] Found java - /usr/local/bin/java
[17:38:19] Found snpEff - /usr/local/bin/snpEff
[17:38:19] Found samclip - /usr/local/bin/samclip
[17:38:19] Found seqtk - /usr/local/bin/seqtk
[17:38:19] Found parallel - /usr/local/bin/parallel
[17:38:19] Found freebayes - /usr/local/bin/freebayes
[17:38:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:38:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:38:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:38:19] Found vcfuniq - /usr/local/bin/vcfuniq
[17:38:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:38:19] Found gzip - /bin/gzip
[17:38:19] Found vt - /usr/local/bin/vt
[17:38:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:38:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:38:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:38:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:38:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:38:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:38:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:38:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [17:38:07] This is snippy 4.6.0Show full stderr[17:38:07] This is snippy 4.6.0
[17:38:07] Written by Torsten Seemann
[17:38:07] Obtained from https://github.com/tseemann/snippy
[17:38:07] Detected operating system: linux
[17:38:07] Enabling bundled linux tools.
[17:38:07] Found bwa - /usr/local/bin/bwa
[17:38:07] Found bcftools - /usr/local/bin/bcftools
[17:38:07] Found samtools - /usr/local/bin/samtools
[17:38:07] Found java - /usr/local/bin/java
[17:38:07] Found snpEff - /usr/local/bin/snpEff
[17:38:07] Found samclip - /usr/local/bin/samclip
[17:38:07] Found seqtk - /usr/local/bin/seqtk
[17:38:07] Found parallel - /usr/local/bin/parallel
[17:38:07] Found freebayes - /usr/local/bin/freebayes
[17:38:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:38:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:38:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:38:07] Found vcfuniq - /usr/local/bin/vcfuniq
[17:38:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:38:07] Found gzip - /bin/gzip
[17:38:07] Found vt - /usr/local/bin/vt
[17:38:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:38:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:38:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:38:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:38:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:38:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:38:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:38:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [00:33:27] This is snippy 4.6.0Show full stderr[00:33:27] This is snippy 4.6.0
[00:33:27] Written by Torsten Seemann
[00:33:27] Obtained from https://github.com/tseemann/snippy
[00:33:27] Detected operating system: linux
[00:33:27] Enabling bundled linux tools.
[00:33:27] Found bwa - /usr/local/bin/bwa
[00:33:27] Found bcftools - /usr/local/bin/bcftools
[00:33:27] Found samtools - /usr/local/bin/samtools
[00:33:27] Found java - /usr/local/bin/java
[00:33:27] Found snpEff - /usr/local/bin/snpEff
[00:33:27] Found samclip - /usr/local/bin/samclip
[00:33:27] Found seqtk - /usr/local/bin/seqtk
[00:33:27] Found parallel - /usr/local/bin/parallel
[00:33:27] Found freebayes - /usr/local/bin/freebayes
[00:33:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:27] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:27] Found gzip - /bin/gzip
[00:33:27] Found vt - /usr/local/bin/vt
[00:33:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [00:54:26] This is snippy 4.6.0Show full stderr[00:54:26] This is snippy 4.6.0
[00:54:26] Written by Torsten Seemann
[00:54:26] Obtained from https://github.com/tseemann/snippy
[00:54:26] Detected operating system: linux
[00:54:26] Enabling bundled linux tools.
[00:54:26] Found bwa - /usr/local/bin/bwa
[00:54:26] Found bcftools - /usr/local/bin/bcftools
[00:54:26] Found samtools - /usr/local/bin/samtools
[00:54:26] Found java - /usr/local/bin/java
[00:54:26] Found snpEff - /usr/local/bin/snpEff
[00:54:26] Found samclip - /usr/local/bin/samclip
[00:54:26] Found seqtk - /usr/local/bin/seqtk
[00:54:26] Found parallel - /usr/local/bin/parallel
[00:54:26] Found freebayes - /usr/local/bin/freebayes
[00:54:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:54:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:54:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:54:26] Found vcfuniq - /usr/local/bin/vcfuniq
[00:54:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:54:26] Found gzip - /bin/gzip
[00:54:26] Found vt - /usr/local/bin/vt
[00:54:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:54:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:54:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:54:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:54:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:54:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:54:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:54:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [08:55:04] This is snippy 4.6.0Show full stderr[08:55:04] This is snippy 4.6.0
[08:55:04] Written by Torsten Seemann
[08:55:04] Obtained from https://github.com/tseemann/snippy
[08:55:04] Detected operating system: linux
[08:55:04] Enabling bundled linux tools.
[08:55:04] Found bwa - /usr/local/bin/bwa
[08:55:04] Found bcftools - /usr/local/bin/bcftools
[08:55:04] Found samtools - /usr/local/bin/samtools
[08:55:04] Found java - /usr/local/bin/java
[08:55:04] Found snpEff - /usr/local/bin/snpEff
[08:55:04] Found samclip - /usr/local/bin/samclip
[08:55:04] Found seqtk - /usr/local/bin/seqtk
[08:55:04] Found parallel - /usr/local/bin/parallel
[08:55:04] Found freebayes - /usr/local/bin/freebayes
[08:55:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:55:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:55:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:55:05] Found vcfuniq - /usr/local/bin/vcfuniq
[08:55:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:55:05] Found gzip - /bin/gzip
[08:55:05] Found vt - /usr/local/bin/vt
[08:55:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:55:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:55:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:55:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:55:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:55:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:55:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:55:06] Using reference: /corral4/main/objects/8/5/7/dataset_85795cef-4d28-485e-8eef-1c59399f6e13.dat
[08:55:09] Treating reference as 'genbank' format.
[08:55:09] Will use 1 CPU cores.
[08:55:09] Using read file: /corral4/main/objects/b/4/0/dataset_b4066cae-0670-4b65-9b32-348e22fbe97f.dat
[08:55:09] Creating folder: PAK_resistant_Strain_zip
[08:55:09] Changing working directory: PAK_resistant_Strain_zip
[08:55:09] Creating reference folder: reference
[08:55:09] Extracting FASTA and GFF from reference.
[08:55:13] Wrote 1 sequences to ref.fa
[08:55:13] Wrote 5867 features to ref.gff
[08:55:13] Creating reference/snpeff.config
[08:55:13] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:55:13] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:55:13] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:55:14] Running: bwa index reference/ref.fa 2>> snps.log
[08:55:21] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[08:55:22] Running: ln -sf reference/ref.fa . 2>> snps.log
[08:55:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[08:55:23] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[08:55:23] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[08:55:33] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/b/4/0/dataset_b4066cae-0670-4b65-9b32-348e22fbe97f.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013863/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013863/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013863/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences in reference/ref.fa.fai
[M::bwa_idx_load_from_di |
| 3 | [21:23:50] This is snippy 4.6.0Show full stderr[21:23:50] This is snippy 4.6.0
[21:23:50] Written by Torsten Seemann
[21:23:50] Obtained from https://github.com/tseemann/snippy
[21:23:50] Detected operating system: linux
[21:23:50] Enabling bundled linux tools.
[21:23:50] Found bwa - /usr/local/bin/bwa
[21:23:50] Found bcftools - /usr/local/bin/bcftools
[21:23:50] Found samtools - /usr/local/bin/samtools
[21:23:50] Found java - /usr/local/bin/java
[21:23:50] Found snpEff - /usr/local/bin/snpEff
[21:23:50] Found samclip - /usr/local/bin/samclip
[21:23:50] Found seqtk - /usr/local/bin/seqtk
[21:23:50] Found parallel - /usr/local/bin/parallel
[21:23:50] Found freebayes - /usr/local/bin/freebayes
[21:23:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:23:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:23:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:23:50] Found vcfuniq - /usr/local/bin/vcfuniq
[21:23:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:23:50] Found gzip - /bin/gzip
[21:23:50] Found vt - /usr/local/bin/vt
[21:23:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:23:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:23:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:23:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:23:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:23:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:23:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:23:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 3 | [05:02:17] This is snippy 4.6.0Show full stderr[05:02:17] This is snippy 4.6.0
[05:02:17] Written by Torsten Seemann
[05:02:17] Obtained from https://github.com/tseemann/snippy
[05:02:17] Detected operating system: linux
[05:02:17] Enabling bundled linux tools.
[05:02:17] Found bwa - /usr/local/bin/bwa
[05:02:17] Found bcftools - /usr/local/bin/bcftools
[05:02:17] Found samtools - /usr/local/bin/samtools
[05:02:17] Found java - /usr/local/bin/java
[05:02:17] Found snpEff - /usr/local/bin/snpEff
[05:02:17] Found samclip - /usr/local/bin/samclip
[05:02:17] Found seqtk - /usr/local/bin/seqtk
[05:02:17] Found parallel - /usr/local/bin/parallel
[05:02:17] Found freebayes - /usr/local/bin/freebayes
[05:02:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:17] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:17] Found gzip - /bin/gzip
[05:02:17] Found vt - /usr/local/bin/vt
[05:02:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [21:23:38] This is snippy 4.6.0Show full stderr[21:23:38] This is snippy 4.6.0
[21:23:38] Written by Torsten Seemann
[21:23:38] Obtained from https://github.com/tseemann/snippy
[21:23:38] Detected operating system: linux
[21:23:38] Enabling bundled linux tools.
[21:23:38] Found bwa - /usr/local/bin/bwa
[21:23:38] Found bcftools - /usr/local/bin/bcftools
[21:23:38] Found samtools - /usr/local/bin/samtools
[21:23:38] Found java - /usr/local/bin/java
[21:23:38] Found snpEff - /usr/local/bin/snpEff
[21:23:38] Found samclip - /usr/local/bin/samclip
[21:23:38] Found seqtk - /usr/local/bin/seqtk
[21:23:38] Found parallel - /usr/local/bin/parallel
[21:23:38] Found freebayes - /usr/local/bin/freebayes
[21:23:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:23:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:23:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:23:38] Found vcfuniq - /usr/local/bin/vcfuniq
[21:23:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:23:38] Found gzip - /bin/gzip
[21:23:38] Found vt - /usr/local/bin/vt
[21:23:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:23:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:23:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:23:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:23:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:23:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:23:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:23:41] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:23:42] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:23:52] This is snippy 4.6.0Show full stderr[21:23:52] This is snippy 4.6.0
[21:23:52] Written by Torsten Seemann
[21:23:52] Obtained from https://github.com/tseemann/snippy
[21:23:52] Detected operating system: linux
[21:23:52] Enabling bundled linux tools.
[21:23:52] Found bwa - /usr/local/bin/bwa
[21:23:52] Found bcftools - /usr/local/bin/bcftools
[21:23:52] Found samtools - /usr/local/bin/samtools
[21:23:52] Found java - /usr/local/bin/java
[21:23:52] Found snpEff - /usr/local/bin/snpEff
[21:23:52] Found samclip - /usr/local/bin/samclip
[21:23:52] Found seqtk - /usr/local/bin/seqtk
[21:23:52] Found parallel - /usr/local/bin/parallel
[21:23:52] Found freebayes - /usr/local/bin/freebayes
[21:23:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:23:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:23:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:23:52] Found vcfuniq - /usr/local/bin/vcfuniq
[21:23:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:23:53] Found gzip - /bin/gzip
[21:23:53] Found vt - /usr/local/bin/vt
[21:23:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:23:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:23:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:23:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:23:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:23:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:23:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:23:54] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:23:54] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:23:55] This is snippy 4.6.0Show full stderr[21:23:55] This is snippy 4.6.0
[21:23:55] Written by Torsten Seemann
[21:23:55] Obtained from https://github.com/tseemann/snippy
[21:23:55] Detected operating system: linux
[21:23:55] Enabling bundled linux tools.
[21:23:55] Found bwa - /usr/local/bin/bwa
[21:23:55] Found bcftools - /usr/local/bin/bcftools
[21:23:55] Found samtools - /usr/local/bin/samtools
[21:23:55] Found java - /usr/local/bin/java
[21:23:55] Found snpEff - /usr/local/bin/snpEff
[21:23:55] Found samclip - /usr/local/bin/samclip
[21:23:55] Found seqtk - /usr/local/bin/seqtk
[21:23:55] Found parallel - /usr/local/bin/parallel
[21:23:56] Found freebayes - /usr/local/bin/freebayes
[21:23:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:23:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:23:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:23:56] Found vcfuniq - /usr/local/bin/vcfuniq
[21:23:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:23:56] Found gzip - /bin/gzip
[21:23:56] Found vt - /usr/local/bin/vt
[21:23:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:23:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:23:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:23:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:23:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:23:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:23:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:23:57] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:23:57] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:24:27] This is snippy 4.6.0Show full stderr[21:24:27] This is snippy 4.6.0
[21:24:27] Written by Torsten Seemann
[21:24:27] Obtained from https://github.com/tseemann/snippy
[21:24:27] Detected operating system: linux
[21:24:27] Enabling bundled linux tools.
[21:24:27] Found bwa - /usr/local/bin/bwa
[21:24:27] Found bcftools - /usr/local/bin/bcftools
[21:24:27] Found samtools - /usr/local/bin/samtools
[21:24:27] Found java - /usr/local/bin/java
[21:24:27] Found snpEff - /usr/local/bin/snpEff
[21:24:27] Found samclip - /usr/local/bin/samclip
[21:24:27] Found seqtk - /usr/local/bin/seqtk
[21:24:27] Found parallel - /usr/local/bin/parallel
[21:24:27] Found freebayes - /usr/local/bin/freebayes
[21:24:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:24:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:24:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:24:27] Found vcfuniq - /usr/local/bin/vcfuniq
[21:24:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:24:27] Found gzip - /bin/gzip
[21:24:27] Found vt - /usr/local/bin/vt
[21:24:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:24:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:24:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:24:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:24:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:24:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:24:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:24:28] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:24:28] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:24:08] This is snippy 4.6.0Show full stderr[21:24:08] This is snippy 4.6.0
[21:24:08] Written by Torsten Seemann
[21:24:08] Obtained from https://github.com/tseemann/snippy
[21:24:08] Detected operating system: linux
[21:24:08] Enabling bundled linux tools.
[21:24:08] Found bwa - /usr/local/bin/bwa
[21:24:08] Found bcftools - /usr/local/bin/bcftools
[21:24:08] Found samtools - /usr/local/bin/samtools
[21:24:08] Found java - /usr/local/bin/java
[21:24:08] Found snpEff - /usr/local/bin/snpEff
[21:24:08] Found samclip - /usr/local/bin/samclip
[21:24:08] Found seqtk - /usr/local/bin/seqtk
[21:24:08] Found parallel - /usr/local/bin/parallel
[21:24:08] Found freebayes - /usr/local/bin/freebayes
[21:24:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:24:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:24:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:24:08] Found vcfuniq - /usr/local/bin/vcfuniq
[21:24:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:24:08] Found gzip - /bin/gzip
[21:24:08] Found vt - /usr/local/bin/vt
[21:24:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:24:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:24:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:24:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:24:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:24:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:24:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:24:09] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:24:09] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:24:48] This is snippy 4.6.0Show full stderr[21:24:48] This is snippy 4.6.0
[21:24:48] Written by Torsten Seemann
[21:24:48] Obtained from https://github.com/tseemann/snippy
[21:24:48] Detected operating system: linux
[21:24:48] Enabling bundled linux tools.
[21:24:48] Found bwa - /usr/local/bin/bwa
[21:24:48] Found bcftools - /usr/local/bin/bcftools
[21:24:48] Found samtools - /usr/local/bin/samtools
[21:24:48] Found java - /usr/local/bin/java
[21:24:48] Found snpEff - /usr/local/bin/snpEff
[21:24:48] Found samclip - /usr/local/bin/samclip
[21:24:48] Found seqtk - /usr/local/bin/seqtk
[21:24:48] Found parallel - /usr/local/bin/parallel
[21:24:48] Found freebayes - /usr/local/bin/freebayes
[21:24:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:24:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:24:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:24:48] Found vcfuniq - /usr/local/bin/vcfuniq
[21:24:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:24:48] Found gzip - /bin/gzip
[21:24:48] Found vt - /usr/local/bin/vt
[21:24:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:24:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:24:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:24:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:24:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:24:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:24:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:24:49] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:24:49] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:24:50] This is snippy 4.6.0Show full stderr[21:24:50] This is snippy 4.6.0
[21:24:50] Written by Torsten Seemann
[21:24:50] Obtained from https://github.com/tseemann/snippy
[21:24:50] Detected operating system: linux
[21:24:50] Enabling bundled linux tools.
[21:24:50] Found bwa - /usr/local/bin/bwa
[21:24:50] Found bcftools - /usr/local/bin/bcftools
[21:24:50] Found samtools - /usr/local/bin/samtools
[21:24:50] Found java - /usr/local/bin/java
[21:24:50] Found snpEff - /usr/local/bin/snpEff
[21:24:50] Found samclip - /usr/local/bin/samclip
[21:24:50] Found seqtk - /usr/local/bin/seqtk
[21:24:50] Found parallel - /usr/local/bin/parallel
[21:24:50] Found freebayes - /usr/local/bin/freebayes
[21:24:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:24:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:24:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:24:50] Found vcfuniq - /usr/local/bin/vcfuniq
[21:24:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:24:50] Found gzip - /bin/gzip
[21:24:50] Found vt - /usr/local/bin/vt
[21:24:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:24:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:24:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:24:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:24:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:24:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:24:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:24:51] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:24:52] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:24:57] This is snippy 4.6.0Show full stderr[21:24:57] This is snippy 4.6.0
[21:24:57] Written by Torsten Seemann
[21:24:57] Obtained from https://github.com/tseemann/snippy
[21:24:57] Detected operating system: linux
[21:24:57] Enabling bundled linux tools.
[21:24:57] Found bwa - /usr/local/bin/bwa
[21:24:57] Found bcftools - /usr/local/bin/bcftools
[21:24:57] Found samtools - /usr/local/bin/samtools
[21:24:57] Found java - /usr/local/bin/java
[21:24:57] Found snpEff - /usr/local/bin/snpEff
[21:24:57] Found samclip - /usr/local/bin/samclip
[21:24:57] Found seqtk - /usr/local/bin/seqtk
[21:24:57] Found parallel - /usr/local/bin/parallel
[21:24:57] Found freebayes - /usr/local/bin/freebayes
[21:24:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:24:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:24:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:24:57] Found vcfuniq - /usr/local/bin/vcfuniq
[21:24:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:24:57] Found gzip - /bin/gzip
[21:24:57] Found vt - /usr/local/bin/vt
[21:24:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:24:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:24:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:24:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:24:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:24:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:24:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:24:58] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:24:58] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:25:15] This is snippy 4.6.0Show full stderr[21:25:15] This is snippy 4.6.0
[21:25:15] Written by Torsten Seemann
[21:25:15] Obtained from https://github.com/tseemann/snippy
[21:25:15] Detected operating system: linux
[21:25:15] Enabling bundled linux tools.
[21:25:15] Found bwa - /usr/local/bin/bwa
[21:25:15] Found bcftools - /usr/local/bin/bcftools
[21:25:15] Found samtools - /usr/local/bin/samtools
[21:25:15] Found java - /usr/local/bin/java
[21:25:15] Found snpEff - /usr/local/bin/snpEff
[21:25:15] Found samclip - /usr/local/bin/samclip
[21:25:15] Found seqtk - /usr/local/bin/seqtk
[21:25:15] Found parallel - /usr/local/bin/parallel
[21:25:15] Found freebayes - /usr/local/bin/freebayes
[21:25:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:25:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:25:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:25:15] Found vcfuniq - /usr/local/bin/vcfuniq
[21:25:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:25:15] Found gzip - /bin/gzip
[21:25:15] Found vt - /usr/local/bin/vt
[21:25:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:25:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:25:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:25:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:25:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:25:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:25:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:25:16] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:25:16] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:34:12] This is snippy 4.6.0Show full stderr[21:34:12] This is snippy 4.6.0
[21:34:12] Written by Torsten Seemann
[21:34:12] Obtained from https://github.com/tseemann/snippy
[21:34:12] Detected operating system: linux
[21:34:12] Enabling bundled linux tools.
[21:34:12] Found bwa - /usr/local/bin/bwa
[21:34:12] Found bcftools - /usr/local/bin/bcftools
[21:34:12] Found samtools - /usr/local/bin/samtools
[21:34:12] Found java - /usr/local/bin/java
[21:34:12] Found snpEff - /usr/local/bin/snpEff
[21:34:12] Found samclip - /usr/local/bin/samclip
[21:34:12] Found seqtk - /usr/local/bin/seqtk
[21:34:12] Found parallel - /usr/local/bin/parallel
[21:34:12] Found freebayes - /usr/local/bin/freebayes
[21:34:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:34:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:34:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:34:12] Found vcfuniq - /usr/local/bin/vcfuniq
[21:34:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:34:12] Found gzip - /bin/gzip
[21:34:12] Found vt - /usr/local/bin/vt
[21:34:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:34:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:34:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:34:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:34:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:34:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:34:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:34:13] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:34:13] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:34:42] This is snippy 4.6.0Show full stderr[21:34:42] This is snippy 4.6.0
[21:34:42] Written by Torsten Seemann
[21:34:42] Obtained from https://github.com/tseemann/snippy
[21:34:42] Detected operating system: linux
[21:34:42] Enabling bundled linux tools.
[21:34:42] Found bwa - /usr/local/bin/bwa
[21:34:42] Found bcftools - /usr/local/bin/bcftools
[21:34:42] Found samtools - /usr/local/bin/samtools
[21:34:42] Found java - /usr/local/bin/java
[21:34:42] Found snpEff - /usr/local/bin/snpEff
[21:34:42] Found samclip - /usr/local/bin/samclip
[21:34:42] Found seqtk - /usr/local/bin/seqtk
[21:34:42] Found parallel - /usr/local/bin/parallel
[21:34:42] Found freebayes - /usr/local/bin/freebayes
[21:34:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:34:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:34:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:34:42] Found vcfuniq - /usr/local/bin/vcfuniq
[21:34:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:34:42] Found gzip - /bin/gzip
[21:34:42] Found vt - /usr/local/bin/vt
[21:34:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:34:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:34:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:34:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:34:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:34:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:34:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:34:43] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:34:43] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:35:05] This is snippy 4.6.0Show full stderr[21:35:05] This is snippy 4.6.0
[21:35:05] Written by Torsten Seemann
[21:35:05] Obtained from https://github.com/tseemann/snippy
[21:35:05] Detected operating system: linux
[21:35:05] Enabling bundled linux tools.
[21:35:05] Found bwa - /usr/local/bin/bwa
[21:35:05] Found bcftools - /usr/local/bin/bcftools
[21:35:05] Found samtools - /usr/local/bin/samtools
[21:35:05] Found java - /usr/local/bin/java
[21:35:05] Found snpEff - /usr/local/bin/snpEff
[21:35:05] Found samclip - /usr/local/bin/samclip
[21:35:05] Found seqtk - /usr/local/bin/seqtk
[21:35:05] Found parallel - /usr/local/bin/parallel
[21:35:05] Found freebayes - /usr/local/bin/freebayes
[21:35:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:35:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:35:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:35:05] Found vcfuniq - /usr/local/bin/vcfuniq
[21:35:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:35:05] Found gzip - /bin/gzip
[21:35:05] Found vt - /usr/local/bin/vt
[21:35:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:35:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:35:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:35:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:35:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:35:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:35:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:35:06] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:35:06] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [21:35:29] This is snippy 4.6.0Show full stderr[21:35:29] This is snippy 4.6.0
[21:35:29] Written by Torsten Seemann
[21:35:29] Obtained from https://github.com/tseemann/snippy
[21:35:29] Detected operating system: linux
[21:35:29] Enabling bundled linux tools.
[21:35:29] Found bwa - /usr/local/bin/bwa
[21:35:29] Found bcftools - /usr/local/bin/bcftools
[21:35:29] Found samtools - /usr/local/bin/samtools
[21:35:29] Found java - /usr/local/bin/java
[21:35:29] Found snpEff - /usr/local/bin/snpEff
[21:35:29] Found samclip - /usr/local/bin/samclip
[21:35:29] Found seqtk - /usr/local/bin/seqtk
[21:35:29] Found parallel - /usr/local/bin/parallel
[21:35:29] Found freebayes - /usr/local/bin/freebayes
[21:35:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:35:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:35:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:35:29] Found vcfuniq - /usr/local/bin/vcfuniq
[21:35:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:35:29] Found gzip - /bin/gzip
[21:35:29] Found vt - /usr/local/bin/vt
[21:35:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:35:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:35:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:35:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:35:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:35:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:35:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:35:31] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:35:31] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 2 | [04:36:43] This is snippy 4.6.0Show full stderr[04:36:43] This is snippy 4.6.0
[04:36:43] Written by Torsten Seemann
[04:36:43] Obtained from https://github.com/tseemann/snippy
[04:36:43] Detected operating system: linux
[04:36:43] Enabling bundled linux tools.
[04:36:43] Found bwa - /usr/local/bin/bwa
[04:36:43] Found bcftools - /usr/local/bin/bcftools
[04:36:43] Found samtools - /usr/local/bin/samtools
[04:36:43] Found java - /usr/local/bin/java
[04:36:43] Found snpEff - /usr/local/bin/snpEff
[04:36:43] Found samclip - /usr/local/bin/samclip
[04:36:43] Found seqtk - /usr/local/bin/seqtk
[04:36:43] Found parallel - /usr/local/bin/parallel
[04:36:43] Found freebayes - /usr/local/bin/freebayes
[04:36:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:36:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:36:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:36:43] Found vcfuniq - /usr/local/bin/vcfuniq
[04:36:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:36:43] Found gzip - /bin/gzip
[04:36:43] Found vt - /usr/local/bin/vt
[04:36:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:36:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:36:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:36:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:36:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:36:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:36:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:36:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:37:39] This is snippy 4.6.0Show full stderr[04:37:39] This is snippy 4.6.0
[04:37:39] Written by Torsten Seemann
[04:37:39] Obtained from https://github.com/tseemann/snippy
[04:37:39] Detected operating system: linux
[04:37:39] Enabling bundled linux tools.
[04:37:39] Found bwa - /usr/local/bin/bwa
[04:37:39] Found bcftools - /usr/local/bin/bcftools
[04:37:39] Found samtools - /usr/local/bin/samtools
[04:37:39] Found java - /usr/local/bin/java
[04:37:39] Found snpEff - /usr/local/bin/snpEff
[04:37:39] Found samclip - /usr/local/bin/samclip
[04:37:39] Found seqtk - /usr/local/bin/seqtk
[04:37:39] Found parallel - /usr/local/bin/parallel
[04:37:39] Found freebayes - /usr/local/bin/freebayes
[04:37:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:39] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:39] Found gzip - /bin/gzip
[04:37:39] Found vt - /usr/local/bin/vt
[04:37:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:38:30] This is snippy 4.6.0Show full stderr[04:38:30] This is snippy 4.6.0
[04:38:30] Written by Torsten Seemann
[04:38:30] Obtained from https://github.com/tseemann/snippy
[04:38:30] Detected operating system: linux
[04:38:30] Enabling bundled linux tools.
[04:38:30] Found bwa - /usr/local/bin/bwa
[04:38:30] Found bcftools - /usr/local/bin/bcftools
[04:38:30] Found samtools - /usr/local/bin/samtools
[04:38:30] Found java - /usr/local/bin/java
[04:38:30] Found snpEff - /usr/local/bin/snpEff
[04:38:30] Found samclip - /usr/local/bin/samclip
[04:38:30] Found seqtk - /usr/local/bin/seqtk
[04:38:30] Found parallel - /usr/local/bin/parallel
[04:38:30] Found freebayes - /usr/local/bin/freebayes
[04:38:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:30] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:30] Found gzip - /bin/gzip
[04:38:30] Found vt - /usr/local/bin/vt
[04:38:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:38:36] This is snippy 4.6.0Show full stderr[04:38:36] This is snippy 4.6.0
[04:38:36] Written by Torsten Seemann
[04:38:36] Obtained from https://github.com/tseemann/snippy
[04:38:36] Detected operating system: linux
[04:38:36] Enabling bundled linux tools.
[04:38:36] Found bwa - /usr/local/bin/bwa
[04:38:36] Found bcftools - /usr/local/bin/bcftools
[04:38:36] Found samtools - /usr/local/bin/samtools
[04:38:36] Found java - /usr/local/bin/java
[04:38:36] Found snpEff - /usr/local/bin/snpEff
[04:38:36] Found samclip - /usr/local/bin/samclip
[04:38:36] Found seqtk - /usr/local/bin/seqtk
[04:38:36] Found parallel - /usr/local/bin/parallel
[04:38:36] Found freebayes - /usr/local/bin/freebayes
[04:38:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:36] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:36] Found gzip - /bin/gzip
[04:38:36] Found vt - /usr/local/bin/vt
[04:38:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:38:06] This is snippy 4.6.0Show full stderr[04:38:06] This is snippy 4.6.0
[04:38:06] Written by Torsten Seemann
[04:38:06] Obtained from https://github.com/tseemann/snippy
[04:38:06] Detected operating system: linux
[04:38:06] Enabling bundled linux tools.
[04:38:06] Found bwa - /usr/local/bin/bwa
[04:38:06] Found bcftools - /usr/local/bin/bcftools
[04:38:06] Found samtools - /usr/local/bin/samtools
[04:38:06] Found java - /usr/local/bin/java
[04:38:06] Found snpEff - /usr/local/bin/snpEff
[04:38:06] Found samclip - /usr/local/bin/samclip
[04:38:06] Found seqtk - /usr/local/bin/seqtk
[04:38:06] Found parallel - /usr/local/bin/parallel
[04:38:06] Found freebayes - /usr/local/bin/freebayes
[04:38:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:06] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:06] Found gzip - /bin/gzip
[04:38:06] Found vt - /usr/local/bin/vt
[04:38:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:38:54] This is snippy 4.6.0Show full stderr[04:38:54] This is snippy 4.6.0
[04:38:54] Written by Torsten Seemann
[04:38:54] Obtained from https://github.com/tseemann/snippy
[04:38:54] Detected operating system: linux
[04:38:54] Enabling bundled linux tools.
[04:38:54] Found bwa - /usr/local/bin/bwa
[04:38:54] Found bcftools - /usr/local/bin/bcftools
[04:38:54] Found samtools - /usr/local/bin/samtools
[04:38:54] Found java - /usr/local/bin/java
[04:38:54] Found snpEff - /usr/local/bin/snpEff
[04:38:54] Found samclip - /usr/local/bin/samclip
[04:38:54] Found seqtk - /usr/local/bin/seqtk
[04:38:54] Found parallel - /usr/local/bin/parallel
[04:38:54] Found freebayes - /usr/local/bin/freebayes
[04:38:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:54] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:54] Found gzip - /bin/gzip
[04:38:54] Found vt - /usr/local/bin/vt
[04:38:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:40:06] This is snippy 4.6.0Show full stderr[04:40:06] This is snippy 4.6.0
[04:40:06] Written by Torsten Seemann
[04:40:06] Obtained from https://github.com/tseemann/snippy
[04:40:06] Detected operating system: linux
[04:40:06] Enabling bundled linux tools.
[04:40:06] Found bwa - /usr/local/bin/bwa
[04:40:06] Found bcftools - /usr/local/bin/bcftools
[04:40:06] Found samtools - /usr/local/bin/samtools
[04:40:06] Found java - /usr/local/bin/java
[04:40:06] Found snpEff - /usr/local/bin/snpEff
[04:40:06] Found samclip - /usr/local/bin/samclip
[04:40:06] Found seqtk - /usr/local/bin/seqtk
[04:40:06] Found parallel - /usr/local/bin/parallel
[04:40:06] Found freebayes - /usr/local/bin/freebayes
[04:40:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:06] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:06] Found gzip - /bin/gzip
[04:40:06] Found vt - /usr/local/bin/vt
[04:40:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:40:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:40:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:40:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:37:42] This is snippy 4.6.0Show full stderr[04:37:42] This is snippy 4.6.0
[04:37:42] Written by Torsten Seemann
[04:37:42] Obtained from https://github.com/tseemann/snippy
[04:37:42] Detected operating system: linux
[04:37:42] Enabling bundled linux tools.
[04:37:42] Found bwa - /usr/local/bin/bwa
[04:37:42] Found bcftools - /usr/local/bin/bcftools
[04:37:42] Found samtools - /usr/local/bin/samtools
[04:37:42] Found java - /usr/local/bin/java
[04:37:42] Found snpEff - /usr/local/bin/snpEff
[04:37:42] Found samclip - /usr/local/bin/samclip
[04:37:42] Found seqtk - /usr/local/bin/seqtk
[04:37:42] Found parallel - /usr/local/bin/parallel
[04:37:42] Found freebayes - /usr/local/bin/freebayes
[04:37:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:42] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:42] Found gzip - /bin/gzip
[04:37:42] Found vt - /usr/local/bin/vt
[04:37:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:38:12] This is snippy 4.6.0Show full stderr[04:38:12] This is snippy 4.6.0
[04:38:12] Written by Torsten Seemann
[04:38:12] Obtained from https://github.com/tseemann/snippy
[04:38:12] Detected operating system: linux
[04:38:12] Enabling bundled linux tools.
[04:38:12] Found bwa - /usr/local/bin/bwa
[04:38:12] Found bcftools - /usr/local/bin/bcftools
[04:38:12] Found samtools - /usr/local/bin/samtools
[04:38:12] Found java - /usr/local/bin/java
[04:38:12] Found snpEff - /usr/local/bin/snpEff
[04:38:12] Found samclip - /usr/local/bin/samclip
[04:38:12] Found seqtk - /usr/local/bin/seqtk
[04:38:12] Found parallel - /usr/local/bin/parallel
[04:38:12] Found freebayes - /usr/local/bin/freebayes
[04:38:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:12] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:12] Found gzip - /bin/gzip
[04:38:12] Found vt - /usr/local/bin/vt
[04:38:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:38:51] This is snippy 4.6.0Show full stderr[04:38:51] This is snippy 4.6.0
[04:38:51] Written by Torsten Seemann
[04:38:51] Obtained from https://github.com/tseemann/snippy
[04:38:51] Detected operating system: linux
[04:38:51] Enabling bundled linux tools.
[04:38:51] Found bwa - /usr/local/bin/bwa
[04:38:51] Found bcftools - /usr/local/bin/bcftools
[04:38:51] Found samtools - /usr/local/bin/samtools
[04:38:51] Found java - /usr/local/bin/java
[04:38:51] Found snpEff - /usr/local/bin/snpEff
[04:38:51] Found samclip - /usr/local/bin/samclip
[04:38:51] Found seqtk - /usr/local/bin/seqtk
[04:38:51] Found parallel - /usr/local/bin/parallel
[04:38:51] Found freebayes - /usr/local/bin/freebayes
[04:38:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:51] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:51] Found gzip - /bin/gzip
[04:38:51] Found vt - /usr/local/bin/vt
[04:38:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:39:06] This is snippy 4.6.0Show full stderr[04:39:06] This is snippy 4.6.0
[04:39:06] Written by Torsten Seemann
[04:39:06] Obtained from https://github.com/tseemann/snippy
[04:39:06] Detected operating system: linux
[04:39:06] Enabling bundled linux tools.
[04:39:06] Found bwa - /usr/local/bin/bwa
[04:39:06] Found bcftools - /usr/local/bin/bcftools
[04:39:06] Found samtools - /usr/local/bin/samtools
[04:39:06] Found java - /usr/local/bin/java
[04:39:06] Found snpEff - /usr/local/bin/snpEff
[04:39:06] Found samclip - /usr/local/bin/samclip
[04:39:06] Found seqtk - /usr/local/bin/seqtk
[04:39:06] Found parallel - /usr/local/bin/parallel
[04:39:06] Found freebayes - /usr/local/bin/freebayes
[04:39:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:39:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:39:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:39:06] Found vcfuniq - /usr/local/bin/vcfuniq
[04:39:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:39:06] Found gzip - /bin/gzip
[04:39:06] Found vt - /usr/local/bin/vt
[04:39:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:39:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:39:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:39:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:39:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:39:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:39:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:39:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:40:12] This is snippy 4.6.0Show full stderr[04:40:12] This is snippy 4.6.0
[04:40:12] Written by Torsten Seemann
[04:40:12] Obtained from https://github.com/tseemann/snippy
[04:40:12] Detected operating system: linux
[04:40:12] Enabling bundled linux tools.
[04:40:12] Found bwa - /usr/local/bin/bwa
[04:40:12] Found bcftools - /usr/local/bin/bcftools
[04:40:12] Found samtools - /usr/local/bin/samtools
[04:40:12] Found java - /usr/local/bin/java
[04:40:12] Found snpEff - /usr/local/bin/snpEff
[04:40:12] Found samclip - /usr/local/bin/samclip
[04:40:12] Found seqtk - /usr/local/bin/seqtk
[04:40:12] Found parallel - /usr/local/bin/parallel
[04:40:12] Found freebayes - /usr/local/bin/freebayes
[04:40:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:12] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:12] Found gzip - /bin/gzip
[04:40:12] Found vt - /usr/local/bin/vt
[04:40:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:40:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:40:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:40:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:39:36] This is snippy 4.6.0Show full stderr[04:39:36] This is snippy 4.6.0
[04:39:36] Written by Torsten Seemann
[04:39:36] Obtained from https://github.com/tseemann/snippy
[04:39:36] Detected operating system: linux
[04:39:36] Enabling bundled linux tools.
[04:39:36] Found bwa - /usr/local/bin/bwa
[04:39:36] Found bcftools - /usr/local/bin/bcftools
[04:39:36] Found samtools - /usr/local/bin/samtools
[04:39:36] Found java - /usr/local/bin/java
[04:39:36] Found snpEff - /usr/local/bin/snpEff
[04:39:36] Found samclip - /usr/local/bin/samclip
[04:39:36] Found seqtk - /usr/local/bin/seqtk
[04:39:36] Found parallel - /usr/local/bin/parallel
[04:39:36] Found freebayes - /usr/local/bin/freebayes
[04:39:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:39:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:39:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:39:36] Found vcfuniq - /usr/local/bin/vcfuniq
[04:39:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:39:36] Found gzip - /bin/gzip
[04:39:36] Found vt - /usr/local/bin/vt
[04:39:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:39:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:39:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:39:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:39:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:39:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:39:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:39:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:39:51] This is snippy 4.6.0Show full stderr[04:39:51] This is snippy 4.6.0
[04:39:51] Written by Torsten Seemann
[04:39:51] Obtained from https://github.com/tseemann/snippy
[04:39:51] Detected operating system: linux
[04:39:51] Enabling bundled linux tools.
[04:39:51] Found bwa - /usr/local/bin/bwa
[04:39:51] Found bcftools - /usr/local/bin/bcftools
[04:39:51] Found samtools - /usr/local/bin/samtools
[04:39:51] Found java - /usr/local/bin/java
[04:39:51] Found snpEff - /usr/local/bin/snpEff
[04:39:51] Found samclip - /usr/local/bin/samclip
[04:39:51] Found seqtk - /usr/local/bin/seqtk
[04:39:51] Found parallel - /usr/local/bin/parallel
[04:39:51] Found freebayes - /usr/local/bin/freebayes
[04:39:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:39:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:39:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:39:51] Found vcfuniq - /usr/local/bin/vcfuniq
[04:39:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:39:51] Found gzip - /bin/gzip
[04:39:51] Found vt - /usr/local/bin/vt
[04:39:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:39:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:39:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:39:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:39:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:39:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:39:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:39:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:40:15] This is snippy 4.6.0Show full stderr[04:40:15] This is snippy 4.6.0
[04:40:15] Written by Torsten Seemann
[04:40:15] Obtained from https://github.com/tseemann/snippy
[04:40:15] Detected operating system: linux
[04:40:15] Enabling bundled linux tools.
[04:40:15] Found bwa - /usr/local/bin/bwa
[04:40:15] Found bcftools - /usr/local/bin/bcftools
[04:40:15] Found samtools - /usr/local/bin/samtools
[04:40:15] Found java - /usr/local/bin/java
[04:40:15] Found snpEff - /usr/local/bin/snpEff
[04:40:15] Found samclip - /usr/local/bin/samclip
[04:40:15] Found seqtk - /usr/local/bin/seqtk
[04:40:15] Found parallel - /usr/local/bin/parallel
[04:40:15] Found freebayes - /usr/local/bin/freebayes
[04:40:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:15] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:15] Found gzip - /bin/gzip
[04:40:15] Found vt - /usr/local/bin/vt
[04:40:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:40:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:40:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:40:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:40:21] This is snippy 4.6.0Show full stderr[04:40:21] This is snippy 4.6.0
[04:40:21] Written by Torsten Seemann
[04:40:21] Obtained from https://github.com/tseemann/snippy
[04:40:21] Detected operating system: linux
[04:40:21] Enabling bundled linux tools.
[04:40:21] Found bwa - /usr/local/bin/bwa
[04:40:21] Found bcftools - /usr/local/bin/bcftools
[04:40:21] Found samtools - /usr/local/bin/samtools
[04:40:21] Found java - /usr/local/bin/java
[04:40:21] Found snpEff - /usr/local/bin/snpEff
[04:40:21] Found samclip - /usr/local/bin/samclip
[04:40:21] Found seqtk - /usr/local/bin/seqtk
[04:40:21] Found parallel - /usr/local/bin/parallel
[04:40:21] Found freebayes - /usr/local/bin/freebayes
[04:40:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:21] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:21] Found gzip - /bin/gzip
[04:40:21] Found vt - /usr/local/bin/vt
[04:40:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:40:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:40:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:40:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:41:21] This is snippy 4.6.0Show full stderr[04:41:21] This is snippy 4.6.0
[04:41:21] Written by Torsten Seemann
[04:41:21] Obtained from https://github.com/tseemann/snippy
[04:41:21] Detected operating system: linux
[04:41:21] Enabling bundled linux tools.
[04:41:21] Found bwa - /usr/local/bin/bwa
[04:41:21] Found bcftools - /usr/local/bin/bcftools
[04:41:21] Found samtools - /usr/local/bin/samtools
[04:41:21] Found java - /usr/local/bin/java
[04:41:21] Found snpEff - /usr/local/bin/snpEff
[04:41:21] Found samclip - /usr/local/bin/samclip
[04:41:21] Found seqtk - /usr/local/bin/seqtk
[04:41:21] Found parallel - /usr/local/bin/parallel
[04:41:21] Found freebayes - /usr/local/bin/freebayes
[04:41:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:21] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:21] Found gzip - /bin/gzip
[04:41:21] Found vt - /usr/local/bin/vt
[04:41:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:42:00] This is snippy 4.6.0Show full stderr[04:42:00] This is snippy 4.6.0
[04:42:00] Written by Torsten Seemann
[04:42:00] Obtained from https://github.com/tseemann/snippy
[04:42:00] Detected operating system: linux
[04:42:00] Enabling bundled linux tools.
[04:42:00] Found bwa - /usr/local/bin/bwa
[04:42:00] Found bcftools - /usr/local/bin/bcftools
[04:42:00] Found samtools - /usr/local/bin/samtools
[04:42:00] Found java - /usr/local/bin/java
[04:42:00] Found snpEff - /usr/local/bin/snpEff
[04:42:00] Found samclip - /usr/local/bin/samclip
[04:42:00] Found seqtk - /usr/local/bin/seqtk
[04:42:00] Found parallel - /usr/local/bin/parallel
[04:42:00] Found freebayes - /usr/local/bin/freebayes
[04:42:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:00] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:00] Found gzip - /bin/gzip
[04:42:00] Found vt - /usr/local/bin/vt
[04:42:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:41:34] This is snippy 4.6.0Show full stderr[04:41:34] This is snippy 4.6.0
[04:41:34] Written by Torsten Seemann
[04:41:34] Obtained from https://github.com/tseemann/snippy
[04:41:34] Detected operating system: linux
[04:41:34] Enabling bundled linux tools.
[04:41:34] Found bwa - /usr/local/bin/bwa
[04:41:34] Found bcftools - /usr/local/bin/bcftools
[04:41:34] Found samtools - /usr/local/bin/samtools
[04:41:34] Found java - /usr/local/bin/java
[04:41:34] Found snpEff - /usr/local/bin/snpEff
[04:41:34] Found samclip - /usr/local/bin/samclip
[04:41:34] Found seqtk - /usr/local/bin/seqtk
[04:41:34] Found parallel - /usr/local/bin/parallel
[04:41:34] Found freebayes - /usr/local/bin/freebayes
[04:41:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:34] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:34] Found gzip - /bin/gzip
[04:41:34] Found vt - /usr/local/bin/vt
[04:41:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:41:49] This is snippy 4.6.0Show full stderr[04:41:49] This is snippy 4.6.0
[04:41:49] Written by Torsten Seemann
[04:41:49] Obtained from https://github.com/tseemann/snippy
[04:41:49] Detected operating system: linux
[04:41:49] Enabling bundled linux tools.
[04:41:49] Found bwa - /usr/local/bin/bwa
[04:41:49] Found bcftools - /usr/local/bin/bcftools
[04:41:49] Found samtools - /usr/local/bin/samtools
[04:41:49] Found java - /usr/local/bin/java
[04:41:49] Found snpEff - /usr/local/bin/snpEff
[04:41:49] Found samclip - /usr/local/bin/samclip
[04:41:49] Found seqtk - /usr/local/bin/seqtk
[04:41:49] Found parallel - /usr/local/bin/parallel
[04:41:49] Found freebayes - /usr/local/bin/freebayes
[04:41:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:49] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:49] Found gzip - /bin/gzip
[04:41:49] Found vt - /usr/local/bin/vt
[04:41:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:42:06] This is snippy 4.6.0Show full stderr[04:42:06] This is snippy 4.6.0
[04:42:06] Written by Torsten Seemann
[04:42:06] Obtained from https://github.com/tseemann/snippy
[04:42:06] Detected operating system: linux
[04:42:06] Enabling bundled linux tools.
[04:42:06] Found bwa - /usr/local/bin/bwa
[04:42:06] Found bcftools - /usr/local/bin/bcftools
[04:42:06] Found samtools - /usr/local/bin/samtools
[04:42:06] Found java - /usr/local/bin/java
[04:42:06] Found snpEff - /usr/local/bin/snpEff
[04:42:06] Found samclip - /usr/local/bin/samclip
[04:42:06] Found seqtk - /usr/local/bin/seqtk
[04:42:06] Found parallel - /usr/local/bin/parallel
[04:42:06] Found freebayes - /usr/local/bin/freebayes
[04:42:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:06] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:06] Found gzip - /bin/gzip
[04:42:06] Found vt - /usr/local/bin/vt
[04:42:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:42:33] This is snippy 4.6.0Show full stderr[04:42:33] This is snippy 4.6.0
[04:42:33] Written by Torsten Seemann
[04:42:33] Obtained from https://github.com/tseemann/snippy
[04:42:33] Detected operating system: linux
[04:42:33] Enabling bundled linux tools.
[04:42:33] Found bwa - /usr/local/bin/bwa
[04:42:33] Found bcftools - /usr/local/bin/bcftools
[04:42:33] Found samtools - /usr/local/bin/samtools
[04:42:33] Found java - /usr/local/bin/java
[04:42:33] Found snpEff - /usr/local/bin/snpEff
[04:42:33] Found samclip - /usr/local/bin/samclip
[04:42:33] Found seqtk - /usr/local/bin/seqtk
[04:42:33] Found parallel - /usr/local/bin/parallel
[04:42:33] Found freebayes - /usr/local/bin/freebayes
[04:42:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:33] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:33] Found gzip - /bin/gzip
[04:42:33] Found vt - /usr/local/bin/vt
[04:42:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:40:32] This is snippy 4.6.0Show full stderr[04:40:32] This is snippy 4.6.0
[04:40:32] Written by Torsten Seemann
[04:40:32] Obtained from https://github.com/tseemann/snippy
[04:40:32] Detected operating system: linux
[04:40:32] Enabling bundled linux tools.
[04:40:32] Found bwa - /usr/local/bin/bwa
[04:40:32] Found bcftools - /usr/local/bin/bcftools
[04:40:32] Found samtools - /usr/local/bin/samtools
[04:40:32] Found java - /usr/local/bin/java
[04:40:32] Found snpEff - /usr/local/bin/snpEff
[04:40:32] Found samclip - /usr/local/bin/samclip
[04:40:32] Found seqtk - /usr/local/bin/seqtk
[04:40:32] Found parallel - /usr/local/bin/parallel
[04:40:32] Found freebayes - /usr/local/bin/freebayes
[04:40:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:32] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:32] Found gzip - /bin/gzip
[04:40:32] Found vt - /usr/local/bin/vt
[04:40:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:40:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:40:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:40:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:40:50] This is snippy 4.6.0Show full stderr[04:40:50] This is snippy 4.6.0
[04:40:50] Written by Torsten Seemann
[04:40:50] Obtained from https://github.com/tseemann/snippy
[04:40:50] Detected operating system: linux
[04:40:50] Enabling bundled linux tools.
[04:40:50] Found bwa - /usr/local/bin/bwa
[04:40:50] Found bcftools - /usr/local/bin/bcftools
[04:40:50] Found samtools - /usr/local/bin/samtools
[04:40:50] Found java - /usr/local/bin/java
[04:40:50] Found snpEff - /usr/local/bin/snpEff
[04:40:50] Found samclip - /usr/local/bin/samclip
[04:40:50] Found seqtk - /usr/local/bin/seqtk
[04:40:50] Found parallel - /usr/local/bin/parallel
[04:40:50] Found freebayes - /usr/local/bin/freebayes
[04:40:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:50] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:50] Found gzip - /bin/gzip
[04:40:50] Found vt - /usr/local/bin/vt
[04:40:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:40:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:40:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:40:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:41:37] This is snippy 4.6.0Show full stderr[04:41:37] This is snippy 4.6.0
[04:41:37] Written by Torsten Seemann
[04:41:37] Obtained from https://github.com/tseemann/snippy
[04:41:37] Detected operating system: linux
[04:41:37] Enabling bundled linux tools.
[04:41:37] Found bwa - /usr/local/bin/bwa
[04:41:37] Found bcftools - /usr/local/bin/bcftools
[04:41:37] Found samtools - /usr/local/bin/samtools
[04:41:37] Found java - /usr/local/bin/java
[04:41:37] Found snpEff - /usr/local/bin/snpEff
[04:41:37] Found samclip - /usr/local/bin/samclip
[04:41:37] Found seqtk - /usr/local/bin/seqtk
[04:41:37] Found parallel - /usr/local/bin/parallel
[04:41:37] Found freebayes - /usr/local/bin/freebayes
[04:41:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:37] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:37] Found gzip - /bin/gzip
[04:41:37] Found vt - /usr/local/bin/vt
[04:41:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:42:03] This is snippy 4.6.0Show full stderr[04:42:03] This is snippy 4.6.0
[04:42:03] Written by Torsten Seemann
[04:42:03] Obtained from https://github.com/tseemann/snippy
[04:42:03] Detected operating system: linux
[04:42:03] Enabling bundled linux tools.
[04:42:03] Found bwa - /usr/local/bin/bwa
[04:42:03] Found bcftools - /usr/local/bin/bcftools
[04:42:03] Found samtools - /usr/local/bin/samtools
[04:42:03] Found java - /usr/local/bin/java
[04:42:03] Found snpEff - /usr/local/bin/snpEff
[04:42:03] Found samclip - /usr/local/bin/samclip
[04:42:03] Found seqtk - /usr/local/bin/seqtk
[04:42:03] Found parallel - /usr/local/bin/parallel
[04:42:03] Found freebayes - /usr/local/bin/freebayes
[04:42:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:03] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:03] Found gzip - /bin/gzip
[04:42:03] Found vt - /usr/local/bin/vt
[04:42:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:42:57] This is snippy 4.6.0Show full stderr[04:42:57] This is snippy 4.6.0
[04:42:57] Written by Torsten Seemann
[04:42:57] Obtained from https://github.com/tseemann/snippy
[04:42:57] Detected operating system: linux
[04:42:57] Enabling bundled linux tools.
[04:42:57] Found bwa - /usr/local/bin/bwa
[04:42:57] Found bcftools - /usr/local/bin/bcftools
[04:42:57] Found samtools - /usr/local/bin/samtools
[04:42:57] Found java - /usr/local/bin/java
[04:42:57] Found snpEff - /usr/local/bin/snpEff
[04:42:57] Found samclip - /usr/local/bin/samclip
[04:42:57] Found seqtk - /usr/local/bin/seqtk
[04:42:57] Found parallel - /usr/local/bin/parallel
[04:42:57] Found freebayes - /usr/local/bin/freebayes
[04:42:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:57] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:57] Found gzip - /bin/gzip
[04:42:57] Found vt - /usr/local/bin/vt
[04:42:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:43:09] This is snippy 4.6.0Show full stderr[04:43:09] This is snippy 4.6.0
[04:43:09] Written by Torsten Seemann
[04:43:09] Obtained from https://github.com/tseemann/snippy
[04:43:09] Detected operating system: linux
[04:43:09] Enabling bundled linux tools.
[04:43:09] Found bwa - /usr/local/bin/bwa
[04:43:09] Found bcftools - /usr/local/bin/bcftools
[04:43:09] Found samtools - /usr/local/bin/samtools
[04:43:09] Found java - /usr/local/bin/java
[04:43:09] Found snpEff - /usr/local/bin/snpEff
[04:43:09] Found samclip - /usr/local/bin/samclip
[04:43:09] Found seqtk - /usr/local/bin/seqtk
[04:43:09] Found parallel - /usr/local/bin/parallel
[04:43:09] Found freebayes - /usr/local/bin/freebayes
[04:43:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:09] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:09] Found gzip - /bin/gzip
[04:43:09] Found vt - /usr/local/bin/vt
[04:43:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:43:49] This is snippy 4.6.0Show full stderr[04:43:49] This is snippy 4.6.0
[04:43:49] Written by Torsten Seemann
[04:43:49] Obtained from https://github.com/tseemann/snippy
[04:43:49] Detected operating system: linux
[04:43:49] Enabling bundled linux tools.
[04:43:49] Found bwa - /usr/local/bin/bwa
[04:43:49] Found bcftools - /usr/local/bin/bcftools
[04:43:49] Found samtools - /usr/local/bin/samtools
[04:43:49] Found java - /usr/local/bin/java
[04:43:49] Found snpEff - /usr/local/bin/snpEff
[04:43:49] Found samclip - /usr/local/bin/samclip
[04:43:49] Found seqtk - /usr/local/bin/seqtk
[04:43:49] Found parallel - /usr/local/bin/parallel
[04:43:49] Found freebayes - /usr/local/bin/freebayes
[04:43:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:49] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:49] Found gzip - /bin/gzip
[04:43:49] Found vt - /usr/local/bin/vt
[04:43:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:44:01] This is snippy 4.6.0Show full stderr[04:44:01] This is snippy 4.6.0
[04:44:01] Written by Torsten Seemann
[04:44:01] Obtained from https://github.com/tseemann/snippy
[04:44:01] Detected operating system: linux
[04:44:01] Enabling bundled linux tools.
[04:44:01] Found bwa - /usr/local/bin/bwa
[04:44:01] Found bcftools - /usr/local/bin/bcftools
[04:44:01] Found samtools - /usr/local/bin/samtools
[04:44:01] Found java - /usr/local/bin/java
[04:44:01] Found snpEff - /usr/local/bin/snpEff
[04:44:01] Found samclip - /usr/local/bin/samclip
[04:44:01] Found seqtk - /usr/local/bin/seqtk
[04:44:01] Found parallel - /usr/local/bin/parallel
[04:44:01] Found freebayes - /usr/local/bin/freebayes
[04:44:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:01] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:01] Found gzip - /bin/gzip
[04:44:01] Found vt - /usr/local/bin/vt
[04:44:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:44:10] This is snippy 4.6.0Show full stderr[04:44:10] This is snippy 4.6.0
[04:44:10] Written by Torsten Seemann
[04:44:10] Obtained from https://github.com/tseemann/snippy
[04:44:10] Detected operating system: linux
[04:44:10] Enabling bundled linux tools.
[04:44:10] Found bwa - /usr/local/bin/bwa
[04:44:10] Found bcftools - /usr/local/bin/bcftools
[04:44:10] Found samtools - /usr/local/bin/samtools
[04:44:10] Found java - /usr/local/bin/java
[04:44:10] Found snpEff - /usr/local/bin/snpEff
[04:44:10] Found samclip - /usr/local/bin/samclip
[04:44:10] Found seqtk - /usr/local/bin/seqtk
[04:44:10] Found parallel - /usr/local/bin/parallel
[04:44:10] Found freebayes - /usr/local/bin/freebayes
[04:44:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:10] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:10] Found gzip - /bin/gzip
[04:44:10] Found vt - /usr/local/bin/vt
[04:44:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:44:31] This is snippy 4.6.0Show full stderr[04:44:31] This is snippy 4.6.0
[04:44:31] Written by Torsten Seemann
[04:44:31] Obtained from https://github.com/tseemann/snippy
[04:44:31] Detected operating system: linux
[04:44:31] Enabling bundled linux tools.
[04:44:31] Found bwa - /usr/local/bin/bwa
[04:44:31] Found bcftools - /usr/local/bin/bcftools
[04:44:31] Found samtools - /usr/local/bin/samtools
[04:44:31] Found java - /usr/local/bin/java
[04:44:31] Found snpEff - /usr/local/bin/snpEff
[04:44:31] Found samclip - /usr/local/bin/samclip
[04:44:31] Found seqtk - /usr/local/bin/seqtk
[04:44:32] Found parallel - /usr/local/bin/parallel
[04:44:32] Found freebayes - /usr/local/bin/freebayes
[04:44:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:32] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:32] Found gzip - /bin/gzip
[04:44:32] Found vt - /usr/local/bin/vt
[04:44:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:44:13] This is snippy 4.6.0Show full stderr[04:44:13] This is snippy 4.6.0
[04:44:13] Written by Torsten Seemann
[04:44:13] Obtained from https://github.com/tseemann/snippy
[04:44:13] Detected operating system: linux
[04:44:13] Enabling bundled linux tools.
[04:44:13] Found bwa - /usr/local/bin/bwa
[04:44:13] Found bcftools - /usr/local/bin/bcftools
[04:44:13] Found samtools - /usr/local/bin/samtools
[04:44:13] Found java - /usr/local/bin/java
[04:44:13] Found snpEff - /usr/local/bin/snpEff
[04:44:13] Found samclip - /usr/local/bin/samclip
[04:44:13] Found seqtk - /usr/local/bin/seqtk
[04:44:13] Found parallel - /usr/local/bin/parallel
[04:44:13] Found freebayes - /usr/local/bin/freebayes
[04:44:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:13] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:13] Found gzip - /bin/gzip
[04:44:13] Found vt - /usr/local/bin/vt
[04:44:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:44:25] This is snippy 4.6.0Show full stderr[04:44:25] This is snippy 4.6.0
[04:44:25] Written by Torsten Seemann
[04:44:25] Obtained from https://github.com/tseemann/snippy
[04:44:25] Detected operating system: linux
[04:44:25] Enabling bundled linux tools.
[04:44:25] Found bwa - /usr/local/bin/bwa
[04:44:25] Found bcftools - /usr/local/bin/bcftools
[04:44:25] Found samtools - /usr/local/bin/samtools
[04:44:25] Found java - /usr/local/bin/java
[04:44:25] Found snpEff - /usr/local/bin/snpEff
[04:44:25] Found samclip - /usr/local/bin/samclip
[04:44:25] Found seqtk - /usr/local/bin/seqtk
[04:44:25] Found parallel - /usr/local/bin/parallel
[04:44:25] Found freebayes - /usr/local/bin/freebayes
[04:44:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:25] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:25] Found gzip - /bin/gzip
[04:44:25] Found vt - /usr/local/bin/vt
[04:44:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:44:40] This is snippy 4.6.0Show full stderr[04:44:40] This is snippy 4.6.0
[04:44:40] Written by Torsten Seemann
[04:44:40] Obtained from https://github.com/tseemann/snippy
[04:44:40] Detected operating system: linux
[04:44:40] Enabling bundled linux tools.
[04:44:40] Found bwa - /usr/local/bin/bwa
[04:44:40] Found bcftools - /usr/local/bin/bcftools
[04:44:40] Found samtools - /usr/local/bin/samtools
[04:44:40] Found java - /usr/local/bin/java
[04:44:40] Found snpEff - /usr/local/bin/snpEff
[04:44:40] Found samclip - /usr/local/bin/samclip
[04:44:40] Found seqtk - /usr/local/bin/seqtk
[04:44:40] Found parallel - /usr/local/bin/parallel
[04:44:40] Found freebayes - /usr/local/bin/freebayes
[04:44:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:40] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:40] Found gzip - /bin/gzip
[04:44:40] Found vt - /usr/local/bin/vt
[04:44:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:43:37] This is snippy 4.6.0Show full stderr[04:43:37] This is snippy 4.6.0
[04:43:37] Written by Torsten Seemann
[04:43:37] Obtained from https://github.com/tseemann/snippy
[04:43:37] Detected operating system: linux
[04:43:37] Enabling bundled linux tools.
[04:43:37] Found bwa - /usr/local/bin/bwa
[04:43:37] Found bcftools - /usr/local/bin/bcftools
[04:43:37] Found samtools - /usr/local/bin/samtools
[04:43:37] Found java - /usr/local/bin/java
[04:43:37] Found snpEff - /usr/local/bin/snpEff
[04:43:37] Found samclip - /usr/local/bin/samclip
[04:43:37] Found seqtk - /usr/local/bin/seqtk
[04:43:37] Found parallel - /usr/local/bin/parallel
[04:43:37] Found freebayes - /usr/local/bin/freebayes
[04:43:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:37] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:37] Found gzip - /bin/gzip
[04:43:37] Found vt - /usr/local/bin/vt
[04:43:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:42:30] This is snippy 4.6.0Show full stderr[04:42:30] This is snippy 4.6.0
[04:42:30] Written by Torsten Seemann
[04:42:30] Obtained from https://github.com/tseemann/snippy
[04:42:30] Detected operating system: linux
[04:42:30] Enabling bundled linux tools.
[04:42:30] Found bwa - /usr/local/bin/bwa
[04:42:30] Found bcftools - /usr/local/bin/bcftools
[04:42:30] Found samtools - /usr/local/bin/samtools
[04:42:30] Found java - /usr/local/bin/java
[04:42:30] Found snpEff - /usr/local/bin/snpEff
[04:42:30] Found samclip - /usr/local/bin/samclip
[04:42:30] Found seqtk - /usr/local/bin/seqtk
[04:42:30] Found parallel - /usr/local/bin/parallel
[04:42:30] Found freebayes - /usr/local/bin/freebayes
[04:42:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:30] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:30] Found gzip - /bin/gzip
[04:42:30] Found vt - /usr/local/bin/vt
[04:42:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:54:52] This is snippy 4.6.0Show full stderr[04:54:52] This is snippy 4.6.0
[04:54:52] Written by Torsten Seemann
[04:54:52] Obtained from https://github.com/tseemann/snippy
[04:54:52] Detected operating system: linux
[04:54:52] Enabling bundled linux tools.
[04:54:52] Found bwa - /usr/local/bin/bwa
[04:54:52] Found bcftools - /usr/local/bin/bcftools
[04:54:52] Found samtools - /usr/local/bin/samtools
[04:54:52] Found java - /usr/local/bin/java
[04:54:52] Found snpEff - /usr/local/bin/snpEff
[04:54:52] Found samclip - /usr/local/bin/samclip
[04:54:52] Found seqtk - /usr/local/bin/seqtk
[04:54:52] Found parallel - /usr/local/bin/parallel
[04:54:52] Found freebayes - /usr/local/bin/freebayes
[04:54:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:54:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:54:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:54:52] Found vcfuniq - /usr/local/bin/vcfuniq
[04:54:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:54:52] Found gzip - /bin/gzip
[04:54:52] Found vt - /usr/local/bin/vt
[04:54:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:54:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:54:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:54:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:54:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:54:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:54:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:54:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:55:09] This is snippy 4.6.0Show full stderr[04:55:09] This is snippy 4.6.0
[04:55:09] Written by Torsten Seemann
[04:55:09] Obtained from https://github.com/tseemann/snippy
[04:55:09] Detected operating system: linux
[04:55:09] Enabling bundled linux tools.
[04:55:09] Found bwa - /usr/local/bin/bwa
[04:55:09] Found bcftools - /usr/local/bin/bcftools
[04:55:09] Found samtools - /usr/local/bin/samtools
[04:55:09] Found java - /usr/local/bin/java
[04:55:09] Found snpEff - /usr/local/bin/snpEff
[04:55:09] Found samclip - /usr/local/bin/samclip
[04:55:09] Found seqtk - /usr/local/bin/seqtk
[04:55:09] Found parallel - /usr/local/bin/parallel
[04:55:09] Found freebayes - /usr/local/bin/freebayes
[04:55:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:09] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:09] Found gzip - /bin/gzip
[04:55:09] Found vt - /usr/local/bin/vt
[04:55:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:55:49] This is snippy 4.6.0Show full stderr[04:55:49] This is snippy 4.6.0
[04:55:49] Written by Torsten Seemann
[04:55:49] Obtained from https://github.com/tseemann/snippy
[04:55:49] Detected operating system: linux
[04:55:49] Enabling bundled linux tools.
[04:55:49] Found bwa - /usr/local/bin/bwa
[04:55:49] Found bcftools - /usr/local/bin/bcftools
[04:55:49] Found samtools - /usr/local/bin/samtools
[04:55:49] Found java - /usr/local/bin/java
[04:55:49] Found snpEff - /usr/local/bin/snpEff
[04:55:49] Found samclip - /usr/local/bin/samclip
[04:55:49] Found seqtk - /usr/local/bin/seqtk
[04:55:49] Found parallel - /usr/local/bin/parallel
[04:55:49] Found freebayes - /usr/local/bin/freebayes
[04:55:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:49] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:49] Found gzip - /bin/gzip
[04:55:49] Found vt - /usr/local/bin/vt
[04:55:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:57:03] This is snippy 4.6.0Show full stderr[04:57:03] This is snippy 4.6.0
[04:57:03] Written by Torsten Seemann
[04:57:03] Obtained from https://github.com/tseemann/snippy
[04:57:03] Detected operating system: linux
[04:57:03] Enabling bundled linux tools.
[04:57:03] Found bwa - /usr/local/bin/bwa
[04:57:03] Found bcftools - /usr/local/bin/bcftools
[04:57:03] Found samtools - /usr/local/bin/samtools
[04:57:03] Found java - /usr/local/bin/java
[04:57:03] Found snpEff - /usr/local/bin/snpEff
[04:57:03] Found samclip - /usr/local/bin/samclip
[04:57:03] Found seqtk - /usr/local/bin/seqtk
[04:57:03] Found parallel - /usr/local/bin/parallel
[04:57:03] Found freebayes - /usr/local/bin/freebayes
[04:57:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:03] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:03] Found gzip - /bin/gzip
[04:57:03] Found vt - /usr/local/bin/vt
[04:57:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:57:09] This is snippy 4.6.0Show full stderr[04:57:09] This is snippy 4.6.0
[04:57:09] Written by Torsten Seemann
[04:57:09] Obtained from https://github.com/tseemann/snippy
[04:57:09] Detected operating system: linux
[04:57:09] Enabling bundled linux tools.
[04:57:09] Found bwa - /usr/local/bin/bwa
[04:57:09] Found bcftools - /usr/local/bin/bcftools
[04:57:09] Found samtools - /usr/local/bin/samtools
[04:57:09] Found java - /usr/local/bin/java
[04:57:09] Found snpEff - /usr/local/bin/snpEff
[04:57:09] Found samclip - /usr/local/bin/samclip
[04:57:09] Found seqtk - /usr/local/bin/seqtk
[04:57:09] Found parallel - /usr/local/bin/parallel
[04:57:09] Found freebayes - /usr/local/bin/freebayes
[04:57:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:09] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:09] Found gzip - /bin/gzip
[04:57:09] Found vt - /usr/local/bin/vt
[04:57:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:57:30] This is snippy 4.6.0Show full stderr[04:57:30] This is snippy 4.6.0
[04:57:30] Written by Torsten Seemann
[04:57:30] Obtained from https://github.com/tseemann/snippy
[04:57:30] Detected operating system: linux
[04:57:30] Enabling bundled linux tools.
[04:57:30] Found bwa - /usr/local/bin/bwa
[04:57:30] Found bcftools - /usr/local/bin/bcftools
[04:57:30] Found samtools - /usr/local/bin/samtools
[04:57:30] Found java - /usr/local/bin/java
[04:57:30] Found snpEff - /usr/local/bin/snpEff
[04:57:30] Found samclip - /usr/local/bin/samclip
[04:57:30] Found seqtk - /usr/local/bin/seqtk
[04:57:30] Found parallel - /usr/local/bin/parallel
[04:57:30] Found freebayes - /usr/local/bin/freebayes
[04:57:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:30] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:30] Found gzip - /bin/gzip
[04:57:30] Found vt - /usr/local/bin/vt
[04:57:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:57:48] This is snippy 4.6.0Show full stderr[04:57:48] This is snippy 4.6.0
[04:57:48] Written by Torsten Seemann
[04:57:48] Obtained from https://github.com/tseemann/snippy
[04:57:48] Detected operating system: linux
[04:57:48] Enabling bundled linux tools.
[04:57:48] Found bwa - /usr/local/bin/bwa
[04:57:48] Found bcftools - /usr/local/bin/bcftools
[04:57:48] Found samtools - /usr/local/bin/samtools
[04:57:48] Found java - /usr/local/bin/java
[04:57:48] Found snpEff - /usr/local/bin/snpEff
[04:57:48] Found samclip - /usr/local/bin/samclip
[04:57:48] Found seqtk - /usr/local/bin/seqtk
[04:57:48] Found parallel - /usr/local/bin/parallel
[04:57:48] Found freebayes - /usr/local/bin/freebayes
[04:57:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:48] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:49] Found gzip - /bin/gzip
[04:57:49] Found vt - /usr/local/bin/vt
[04:57:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:58:03] This is snippy 4.6.0Show full stderr[04:58:03] This is snippy 4.6.0
[04:58:03] Written by Torsten Seemann
[04:58:03] Obtained from https://github.com/tseemann/snippy
[04:58:03] Detected operating system: linux
[04:58:03] Enabling bundled linux tools.
[04:58:03] Found bwa - /usr/local/bin/bwa
[04:58:03] Found bcftools - /usr/local/bin/bcftools
[04:58:03] Found samtools - /usr/local/bin/samtools
[04:58:03] Found java - /usr/local/bin/java
[04:58:03] Found snpEff - /usr/local/bin/snpEff
[04:58:03] Found samclip - /usr/local/bin/samclip
[04:58:03] Found seqtk - /usr/local/bin/seqtk
[04:58:03] Found parallel - /usr/local/bin/parallel
[04:58:03] Found freebayes - /usr/local/bin/freebayes
[04:58:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:58:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:58:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:58:03] Found vcfuniq - /usr/local/bin/vcfuniq
[04:58:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:58:03] Found gzip - /bin/gzip
[04:58:03] Found vt - /usr/local/bin/vt
[04:58:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:58:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:58:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:58:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:58:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:58:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:58:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:58:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:56:45] This is snippy 4.6.0Show full stderr[04:56:45] This is snippy 4.6.0
[04:56:45] Written by Torsten Seemann
[04:56:45] Obtained from https://github.com/tseemann/snippy
[04:56:45] Detected operating system: linux
[04:56:45] Enabling bundled linux tools.
[04:56:45] Found bwa - /usr/local/bin/bwa
[04:56:45] Found bcftools - /usr/local/bin/bcftools
[04:56:45] Found samtools - /usr/local/bin/samtools
[04:56:45] Found java - /usr/local/bin/java
[04:56:45] Found snpEff - /usr/local/bin/snpEff
[04:56:45] Found samclip - /usr/local/bin/samclip
[04:56:45] Found seqtk - /usr/local/bin/seqtk
[04:56:45] Found parallel - /usr/local/bin/parallel
[04:56:45] Found freebayes - /usr/local/bin/freebayes
[04:56:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:45] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:45] Found gzip - /bin/gzip
[04:56:45] Found vt - /usr/local/bin/vt
[04:56:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:58:21] This is snippy 4.6.0Show full stderr[04:58:21] This is snippy 4.6.0
[04:58:21] Written by Torsten Seemann
[04:58:21] Obtained from https://github.com/tseemann/snippy
[04:58:21] Detected operating system: linux
[04:58:21] Enabling bundled linux tools.
[04:58:21] Found bwa - /usr/local/bin/bwa
[04:58:21] Found bcftools - /usr/local/bin/bcftools
[04:58:21] Found samtools - /usr/local/bin/samtools
[04:58:21] Found java - /usr/local/bin/java
[04:58:21] Found snpEff - /usr/local/bin/snpEff
[04:58:21] Found samclip - /usr/local/bin/samclip
[04:58:21] Found seqtk - /usr/local/bin/seqtk
[04:58:21] Found parallel - /usr/local/bin/parallel
[04:58:21] Found freebayes - /usr/local/bin/freebayes
[04:58:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:58:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:58:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:58:21] Found vcfuniq - /usr/local/bin/vcfuniq
[04:58:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:58:21] Found gzip - /bin/gzip
[04:58:21] Found vt - /usr/local/bin/vt
[04:58:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:58:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:58:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:58:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:58:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:58:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:58:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:58:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:58:33] This is snippy 4.6.0Show full stderr[04:58:33] This is snippy 4.6.0
[04:58:33] Written by Torsten Seemann
[04:58:33] Obtained from https://github.com/tseemann/snippy
[04:58:33] Detected operating system: linux
[04:58:33] Enabling bundled linux tools.
[04:58:33] Found bwa - /usr/local/bin/bwa
[04:58:33] Found bcftools - /usr/local/bin/bcftools
[04:58:33] Found samtools - /usr/local/bin/samtools
[04:58:33] Found java - /usr/local/bin/java
[04:58:33] Found snpEff - /usr/local/bin/snpEff
[04:58:33] Found samclip - /usr/local/bin/samclip
[04:58:33] Found seqtk - /usr/local/bin/seqtk
[04:58:33] Found parallel - /usr/local/bin/parallel
[04:58:33] Found freebayes - /usr/local/bin/freebayes
[04:58:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:58:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:58:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:58:33] Found vcfuniq - /usr/local/bin/vcfuniq
[04:58:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:58:33] Found gzip - /bin/gzip
[04:58:33] Found vt - /usr/local/bin/vt
[04:58:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:58:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:58:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:58:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:58:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:58:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:58:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:58:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:59:06] This is snippy 4.6.0Show full stderr[04:59:06] This is snippy 4.6.0
[04:59:06] Written by Torsten Seemann
[04:59:06] Obtained from https://github.com/tseemann/snippy
[04:59:06] Detected operating system: linux
[04:59:06] Enabling bundled linux tools.
[04:59:06] Found bwa - /usr/local/bin/bwa
[04:59:06] Found bcftools - /usr/local/bin/bcftools
[04:59:06] Found samtools - /usr/local/bin/samtools
[04:59:06] Found java - /usr/local/bin/java
[04:59:06] Found snpEff - /usr/local/bin/snpEff
[04:59:06] Found samclip - /usr/local/bin/samclip
[04:59:06] Found seqtk - /usr/local/bin/seqtk
[04:59:06] Found parallel - /usr/local/bin/parallel
[04:59:06] Found freebayes - /usr/local/bin/freebayes
[04:59:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:06] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:06] Found gzip - /bin/gzip
[04:59:06] Found vt - /usr/local/bin/vt
[04:59:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:56:54] This is snippy 4.6.0Show full stderr[04:56:54] This is snippy 4.6.0
[04:56:54] Written by Torsten Seemann
[04:56:54] Obtained from https://github.com/tseemann/snippy
[04:56:54] Detected operating system: linux
[04:56:54] Enabling bundled linux tools.
[04:56:54] Found bwa - /usr/local/bin/bwa
[04:56:54] Found bcftools - /usr/local/bin/bcftools
[04:56:54] Found samtools - /usr/local/bin/samtools
[04:56:54] Found java - /usr/local/bin/java
[04:56:54] Found snpEff - /usr/local/bin/snpEff
[04:56:54] Found samclip - /usr/local/bin/samclip
[04:56:54] Found seqtk - /usr/local/bin/seqtk
[04:56:54] Found parallel - /usr/local/bin/parallel
[04:56:54] Found freebayes - /usr/local/bin/freebayes
[04:56:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:54] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:54] Found gzip - /bin/gzip
[04:56:54] Found vt - /usr/local/bin/vt
[04:56:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:57:21] This is snippy 4.6.0Show full stderr[04:57:21] This is snippy 4.6.0
[04:57:21] Written by Torsten Seemann
[04:57:21] Obtained from https://github.com/tseemann/snippy
[04:57:21] Detected operating system: linux
[04:57:21] Enabling bundled linux tools.
[04:57:21] Found bwa - /usr/local/bin/bwa
[04:57:21] Found bcftools - /usr/local/bin/bcftools
[04:57:21] Found samtools - /usr/local/bin/samtools
[04:57:21] Found java - /usr/local/bin/java
[04:57:21] Found snpEff - /usr/local/bin/snpEff
[04:57:21] Found samclip - /usr/local/bin/samclip
[04:57:21] Found seqtk - /usr/local/bin/seqtk
[04:57:21] Found parallel - /usr/local/bin/parallel
[04:57:21] Found freebayes - /usr/local/bin/freebayes
[04:57:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:21] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:21] Found gzip - /bin/gzip
[04:57:21] Found vt - /usr/local/bin/vt
[04:57:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:57:24] This is snippy 4.6.0Show full stderr[04:57:24] This is snippy 4.6.0
[04:57:24] Written by Torsten Seemann
[04:57:24] Obtained from https://github.com/tseemann/snippy
[04:57:24] Detected operating system: linux
[04:57:24] Enabling bundled linux tools.
[04:57:24] Found bwa - /usr/local/bin/bwa
[04:57:24] Found bcftools - /usr/local/bin/bcftools
[04:57:24] Found samtools - /usr/local/bin/samtools
[04:57:24] Found java - /usr/local/bin/java
[04:57:24] Found snpEff - /usr/local/bin/snpEff
[04:57:24] Found samclip - /usr/local/bin/samclip
[04:57:24] Found seqtk - /usr/local/bin/seqtk
[04:57:24] Found parallel - /usr/local/bin/parallel
[04:57:24] Found freebayes - /usr/local/bin/freebayes
[04:57:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:24] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:24] Found gzip - /bin/gzip
[04:57:24] Found vt - /usr/local/bin/vt
[04:57:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:58:48] This is snippy 4.6.0Show full stderr[04:58:48] This is snippy 4.6.0
[04:58:48] Written by Torsten Seemann
[04:58:48] Obtained from https://github.com/tseemann/snippy
[04:58:48] Detected operating system: linux
[04:58:48] Enabling bundled linux tools.
[04:58:48] Found bwa - /usr/local/bin/bwa
[04:58:48] Found bcftools - /usr/local/bin/bcftools
[04:58:48] Found samtools - /usr/local/bin/samtools
[04:58:48] Found java - /usr/local/bin/java
[04:58:48] Found snpEff - /usr/local/bin/snpEff
[04:58:48] Found samclip - /usr/local/bin/samclip
[04:58:48] Found seqtk - /usr/local/bin/seqtk
[04:58:48] Found parallel - /usr/local/bin/parallel
[04:58:48] Found freebayes - /usr/local/bin/freebayes
[04:58:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:58:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:58:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:58:48] Found vcfuniq - /usr/local/bin/vcfuniq
[04:58:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:58:48] Found gzip - /bin/gzip
[04:58:48] Found vt - /usr/local/bin/vt
[04:58:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:58:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:58:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:58:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:58:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:58:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:58:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:58:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:59:18] This is snippy 4.6.0Show full stderr[04:59:18] This is snippy 4.6.0
[04:59:18] Written by Torsten Seemann
[04:59:18] Obtained from https://github.com/tseemann/snippy
[04:59:18] Detected operating system: linux
[04:59:18] Enabling bundled linux tools.
[04:59:18] Found bwa - /usr/local/bin/bwa
[04:59:18] Found bcftools - /usr/local/bin/bcftools
[04:59:18] Found samtools - /usr/local/bin/samtools
[04:59:18] Found java - /usr/local/bin/java
[04:59:18] Found snpEff - /usr/local/bin/snpEff
[04:59:18] Found samclip - /usr/local/bin/samclip
[04:59:18] Found seqtk - /usr/local/bin/seqtk
[04:59:18] Found parallel - /usr/local/bin/parallel
[04:59:18] Found freebayes - /usr/local/bin/freebayes
[04:59:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:18] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:18] Found gzip - /bin/gzip
[04:59:18] Found vt - /usr/local/bin/vt
[04:59:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:59:37] This is snippy 4.6.0Show full stderr[04:59:37] This is snippy 4.6.0
[04:59:37] Written by Torsten Seemann
[04:59:37] Obtained from https://github.com/tseemann/snippy
[04:59:37] Detected operating system: linux
[04:59:37] Enabling bundled linux tools.
[04:59:37] Found bwa - /usr/local/bin/bwa
[04:59:37] Found bcftools - /usr/local/bin/bcftools
[04:59:37] Found samtools - /usr/local/bin/samtools
[04:59:37] Found java - /usr/local/bin/java
[04:59:37] Found snpEff - /usr/local/bin/snpEff
[04:59:37] Found samclip - /usr/local/bin/samclip
[04:59:37] Found seqtk - /usr/local/bin/seqtk
[04:59:37] Found parallel - /usr/local/bin/parallel
[04:59:37] Found freebayes - /usr/local/bin/freebayes
[04:59:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:37] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:37] Found gzip - /bin/gzip
[04:59:37] Found vt - /usr/local/bin/vt
[04:59:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:00:01] This is snippy 4.6.0Show full stderr[05:00:01] This is snippy 4.6.0
[05:00:01] Written by Torsten Seemann
[05:00:01] Obtained from https://github.com/tseemann/snippy
[05:00:01] Detected operating system: linux
[05:00:01] Enabling bundled linux tools.
[05:00:01] Found bwa - /usr/local/bin/bwa
[05:00:01] Found bcftools - /usr/local/bin/bcftools
[05:00:01] Found samtools - /usr/local/bin/samtools
[05:00:01] Found java - /usr/local/bin/java
[05:00:01] Found snpEff - /usr/local/bin/snpEff
[05:00:01] Found samclip - /usr/local/bin/samclip
[05:00:01] Found seqtk - /usr/local/bin/seqtk
[05:00:01] Found parallel - /usr/local/bin/parallel
[05:00:01] Found freebayes - /usr/local/bin/freebayes
[05:00:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:01] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:01] Found gzip - /bin/gzip
[05:00:01] Found vt - /usr/local/bin/vt
[05:00:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:56:57] This is snippy 4.6.0Show full stderr[04:56:57] This is snippy 4.6.0
[04:56:57] Written by Torsten Seemann
[04:56:57] Obtained from https://github.com/tseemann/snippy
[04:56:57] Detected operating system: linux
[04:56:57] Enabling bundled linux tools.
[04:56:57] Found bwa - /usr/local/bin/bwa
[04:56:57] Found bcftools - /usr/local/bin/bcftools
[04:56:57] Found samtools - /usr/local/bin/samtools
[04:56:57] Found java - /usr/local/bin/java
[04:56:57] Found snpEff - /usr/local/bin/snpEff
[04:56:57] Found samclip - /usr/local/bin/samclip
[04:56:57] Found seqtk - /usr/local/bin/seqtk
[04:56:57] Found parallel - /usr/local/bin/parallel
[04:56:57] Found freebayes - /usr/local/bin/freebayes
[04:56:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:57] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:57] Found gzip - /bin/gzip
[04:56:57] Found vt - /usr/local/bin/vt
[04:56:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:59:48] This is snippy 4.6.0Show full stderr[04:59:48] This is snippy 4.6.0
[04:59:48] Written by Torsten Seemann
[04:59:48] Obtained from https://github.com/tseemann/snippy
[04:59:48] Detected operating system: linux
[04:59:48] Enabling bundled linux tools.
[04:59:48] Found bwa - /usr/local/bin/bwa
[04:59:48] Found bcftools - /usr/local/bin/bcftools
[04:59:48] Found samtools - /usr/local/bin/samtools
[04:59:48] Found java - /usr/local/bin/java
[04:59:48] Found snpEff - /usr/local/bin/snpEff
[04:59:48] Found samclip - /usr/local/bin/samclip
[04:59:48] Found seqtk - /usr/local/bin/seqtk
[04:59:48] Found parallel - /usr/local/bin/parallel
[04:59:48] Found freebayes - /usr/local/bin/freebayes
[04:59:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:48] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:48] Found gzip - /bin/gzip
[04:59:48] Found vt - /usr/local/bin/vt
[04:59:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:00:15] This is snippy 4.6.0Show full stderr[05:00:15] This is snippy 4.6.0
[05:00:15] Written by Torsten Seemann
[05:00:15] Obtained from https://github.com/tseemann/snippy
[05:00:15] Detected operating system: linux
[05:00:15] Enabling bundled linux tools.
[05:00:15] Found bwa - /usr/local/bin/bwa
[05:00:15] Found bcftools - /usr/local/bin/bcftools
[05:00:15] Found samtools - /usr/local/bin/samtools
[05:00:15] Found java - /usr/local/bin/java
[05:00:15] Found snpEff - /usr/local/bin/snpEff
[05:00:15] Found samclip - /usr/local/bin/samclip
[05:00:15] Found seqtk - /usr/local/bin/seqtk
[05:00:15] Found parallel - /usr/local/bin/parallel
[05:00:15] Found freebayes - /usr/local/bin/freebayes
[05:00:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:15] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:15] Found gzip - /bin/gzip
[05:00:15] Found vt - /usr/local/bin/vt
[05:00:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:01:15] This is snippy 4.6.0Show full stderr[05:01:15] This is snippy 4.6.0
[05:01:15] Written by Torsten Seemann
[05:01:15] Obtained from https://github.com/tseemann/snippy
[05:01:15] Detected operating system: linux
[05:01:15] Enabling bundled linux tools.
[05:01:15] Found bwa - /usr/local/bin/bwa
[05:01:15] Found bcftools - /usr/local/bin/bcftools
[05:01:15] Found samtools - /usr/local/bin/samtools
[05:01:15] Found java - /usr/local/bin/java
[05:01:15] Found snpEff - /usr/local/bin/snpEff
[05:01:15] Found samclip - /usr/local/bin/samclip
[05:01:15] Found seqtk - /usr/local/bin/seqtk
[05:01:15] Found parallel - /usr/local/bin/parallel
[05:01:15] Found freebayes - /usr/local/bin/freebayes
[05:01:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:15] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:15] Found gzip - /bin/gzip
[05:01:15] Found vt - /usr/local/bin/vt
[05:01:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:58:39] This is snippy 4.6.0Show full stderr[04:58:39] This is snippy 4.6.0
[04:58:39] Written by Torsten Seemann
[04:58:39] Obtained from https://github.com/tseemann/snippy
[04:58:39] Detected operating system: linux
[04:58:39] Enabling bundled linux tools.
[04:58:39] Found bwa - /usr/local/bin/bwa
[04:58:39] Found bcftools - /usr/local/bin/bcftools
[04:58:39] Found samtools - /usr/local/bin/samtools
[04:58:39] Found java - /usr/local/bin/java
[04:58:39] Found snpEff - /usr/local/bin/snpEff
[04:58:39] Found samclip - /usr/local/bin/samclip
[04:58:39] Found seqtk - /usr/local/bin/seqtk
[04:58:39] Found parallel - /usr/local/bin/parallel
[04:58:39] Found freebayes - /usr/local/bin/freebayes
[04:58:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:58:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:58:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:58:40] Found vcfuniq - /usr/local/bin/vcfuniq
[04:58:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:58:40] Found gzip - /bin/gzip
[04:58:40] Found vt - /usr/local/bin/vt
[04:58:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:58:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:58:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:58:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:58:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:58:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:58:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:58:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:59:03] This is snippy 4.6.0Show full stderr[04:59:03] This is snippy 4.6.0
[04:59:03] Written by Torsten Seemann
[04:59:03] Obtained from https://github.com/tseemann/snippy
[04:59:03] Detected operating system: linux
[04:59:03] Enabling bundled linux tools.
[04:59:03] Found bwa - /usr/local/bin/bwa
[04:59:03] Found bcftools - /usr/local/bin/bcftools
[04:59:03] Found samtools - /usr/local/bin/samtools
[04:59:03] Found java - /usr/local/bin/java
[04:59:03] Found snpEff - /usr/local/bin/snpEff
[04:59:03] Found samclip - /usr/local/bin/samclip
[04:59:03] Found seqtk - /usr/local/bin/seqtk
[04:59:03] Found parallel - /usr/local/bin/parallel
[04:59:03] Found freebayes - /usr/local/bin/freebayes
[04:59:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:03] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:03] Found gzip - /bin/gzip
[04:59:03] Found vt - /usr/local/bin/vt
[04:59:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:59:33] This is snippy 4.6.0Show full stderr[04:59:33] This is snippy 4.6.0
[04:59:33] Written by Torsten Seemann
[04:59:33] Obtained from https://github.com/tseemann/snippy
[04:59:33] Detected operating system: linux
[04:59:33] Enabling bundled linux tools.
[04:59:33] Found bwa - /usr/local/bin/bwa
[04:59:33] Found bcftools - /usr/local/bin/bcftools
[04:59:33] Found samtools - /usr/local/bin/samtools
[04:59:33] Found java - /usr/local/bin/java
[04:59:33] Found snpEff - /usr/local/bin/snpEff
[04:59:33] Found samclip - /usr/local/bin/samclip
[04:59:33] Found seqtk - /usr/local/bin/seqtk
[04:59:33] Found parallel - /usr/local/bin/parallel
[04:59:33] Found freebayes - /usr/local/bin/freebayes
[04:59:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:33] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:33] Found gzip - /bin/gzip
[04:59:33] Found vt - /usr/local/bin/vt
[04:59:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [04:59:54] This is snippy 4.6.0Show full stderr[04:59:54] This is snippy 4.6.0
[04:59:54] Written by Torsten Seemann
[04:59:54] Obtained from https://github.com/tseemann/snippy
[04:59:54] Detected operating system: linux
[04:59:54] Enabling bundled linux tools.
[04:59:54] Found bwa - /usr/local/bin/bwa
[04:59:54] Found bcftools - /usr/local/bin/bcftools
[04:59:54] Found samtools - /usr/local/bin/samtools
[04:59:54] Found java - /usr/local/bin/java
[04:59:54] Found snpEff - /usr/local/bin/snpEff
[04:59:54] Found samclip - /usr/local/bin/samclip
[04:59:54] Found seqtk - /usr/local/bin/seqtk
[04:59:54] Found parallel - /usr/local/bin/parallel
[04:59:54] Found freebayes - /usr/local/bin/freebayes
[04:59:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:54] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:54] Found gzip - /bin/gzip
[04:59:54] Found vt - /usr/local/bin/vt
[04:59:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:03:03] This is snippy 4.6.0Show full stderr[05:03:03] This is snippy 4.6.0
[05:03:03] Written by Torsten Seemann
[05:03:03] Obtained from https://github.com/tseemann/snippy
[05:03:03] Detected operating system: linux
[05:03:03] Enabling bundled linux tools.
[05:03:03] Found bwa - /usr/local/bin/bwa
[05:03:03] Found bcftools - /usr/local/bin/bcftools
[05:03:03] Found samtools - /usr/local/bin/samtools
[05:03:03] Found java - /usr/local/bin/java
[05:03:03] Found snpEff - /usr/local/bin/snpEff
[05:03:03] Found samclip - /usr/local/bin/samclip
[05:03:03] Found seqtk - /usr/local/bin/seqtk
[05:03:03] Found parallel - /usr/local/bin/parallel
[05:03:03] Found freebayes - /usr/local/bin/freebayes
[05:03:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:03] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:03] Found gzip - /bin/gzip
[05:03:03] Found vt - /usr/local/bin/vt
[05:03:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:04:06] This is snippy 4.6.0Show full stderr[05:04:06] This is snippy 4.6.0
[05:04:06] Written by Torsten Seemann
[05:04:06] Obtained from https://github.com/tseemann/snippy
[05:04:06] Detected operating system: linux
[05:04:06] Enabling bundled linux tools.
[05:04:06] Found bwa - /usr/local/bin/bwa
[05:04:06] Found bcftools - /usr/local/bin/bcftools
[05:04:06] Found samtools - /usr/local/bin/samtools
[05:04:06] Found java - /usr/local/bin/java
[05:04:06] Found snpEff - /usr/local/bin/snpEff
[05:04:06] Found samclip - /usr/local/bin/samclip
[05:04:06] Found seqtk - /usr/local/bin/seqtk
[05:04:06] Found parallel - /usr/local/bin/parallel
[05:04:06] Found freebayes - /usr/local/bin/freebayes
[05:04:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:06] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:06] Found gzip - /bin/gzip
[05:04:06] Found vt - /usr/local/bin/vt
[05:04:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:04:23] This is snippy 4.6.0Show full stderr[05:04:23] This is snippy 4.6.0
[05:04:23] Written by Torsten Seemann
[05:04:23] Obtained from https://github.com/tseemann/snippy
[05:04:23] Detected operating system: linux
[05:04:23] Enabling bundled linux tools.
[05:04:23] Found bwa - /usr/local/bin/bwa
[05:04:23] Found bcftools - /usr/local/bin/bcftools
[05:04:23] Found samtools - /usr/local/bin/samtools
[05:04:23] Found java - /usr/local/bin/java
[05:04:23] Found snpEff - /usr/local/bin/snpEff
[05:04:23] Found samclip - /usr/local/bin/samclip
[05:04:23] Found seqtk - /usr/local/bin/seqtk
[05:04:23] Found parallel - /usr/local/bin/parallel
[05:04:23] Found freebayes - /usr/local/bin/freebayes
[05:04:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:23] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:23] Found gzip - /bin/gzip
[05:04:23] Found vt - /usr/local/bin/vt
[05:04:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:04:32] This is snippy 4.6.0Show full stderr[05:04:32] This is snippy 4.6.0
[05:04:32] Written by Torsten Seemann
[05:04:32] Obtained from https://github.com/tseemann/snippy
[05:04:32] Detected operating system: linux
[05:04:32] Enabling bundled linux tools.
[05:04:32] Found bwa - /usr/local/bin/bwa
[05:04:32] Found bcftools - /usr/local/bin/bcftools
[05:04:32] Found samtools - /usr/local/bin/samtools
[05:04:32] Found java - /usr/local/bin/java
[05:04:32] Found snpEff - /usr/local/bin/snpEff
[05:04:32] Found samclip - /usr/local/bin/samclip
[05:04:32] Found seqtk - /usr/local/bin/seqtk
[05:04:32] Found parallel - /usr/local/bin/parallel
[05:04:32] Found freebayes - /usr/local/bin/freebayes
[05:04:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:32] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:32] Found gzip - /bin/gzip
[05:04:32] Found vt - /usr/local/bin/vt
[05:04:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:01:52] This is snippy 4.6.0Show full stderr[05:01:52] This is snippy 4.6.0
[05:01:52] Written by Torsten Seemann
[05:01:52] Obtained from https://github.com/tseemann/snippy
[05:01:52] Detected operating system: linux
[05:01:52] Enabling bundled linux tools.
[05:01:52] Found bwa - /usr/local/bin/bwa
[05:01:52] Found bcftools - /usr/local/bin/bcftools
[05:01:52] Found samtools - /usr/local/bin/samtools
[05:01:52] Found java - /usr/local/bin/java
[05:01:52] Found snpEff - /usr/local/bin/snpEff
[05:01:52] Found samclip - /usr/local/bin/samclip
[05:01:52] Found seqtk - /usr/local/bin/seqtk
[05:01:52] Found parallel - /usr/local/bin/parallel
[05:01:52] Found freebayes - /usr/local/bin/freebayes
[05:01:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:52] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:52] Found gzip - /bin/gzip
[05:01:52] Found vt - /usr/local/bin/vt
[05:01:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:03:16] This is snippy 4.6.0Show full stderr[05:03:16] This is snippy 4.6.0
[05:03:16] Written by Torsten Seemann
[05:03:16] Obtained from https://github.com/tseemann/snippy
[05:03:16] Detected operating system: linux
[05:03:16] Enabling bundled linux tools.
[05:03:16] Found bwa - /usr/local/bin/bwa
[05:03:16] Found bcftools - /usr/local/bin/bcftools
[05:03:17] Found samtools - /usr/local/bin/samtools
[05:03:17] Found java - /usr/local/bin/java
[05:03:17] Found snpEff - /usr/local/bin/snpEff
[05:03:17] Found samclip - /usr/local/bin/samclip
[05:03:17] Found seqtk - /usr/local/bin/seqtk
[05:03:17] Found parallel - /usr/local/bin/parallel
[05:03:17] Found freebayes - /usr/local/bin/freebayes
[05:03:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:17] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:17] Found gzip - /bin/gzip
[05:03:17] Found vt - /usr/local/bin/vt
[05:03:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:04:17] This is snippy 4.6.0Show full stderr[05:04:17] This is snippy 4.6.0
[05:04:17] Written by Torsten Seemann
[05:04:17] Obtained from https://github.com/tseemann/snippy
[05:04:17] Detected operating system: linux
[05:04:17] Enabling bundled linux tools.
[05:04:17] Found bwa - /usr/local/bin/bwa
[05:04:17] Found bcftools - /usr/local/bin/bcftools
[05:04:17] Found samtools - /usr/local/bin/samtools
[05:04:17] Found java - /usr/local/bin/java
[05:04:17] Found snpEff - /usr/local/bin/snpEff
[05:04:17] Found samclip - /usr/local/bin/samclip
[05:04:17] Found seqtk - /usr/local/bin/seqtk
[05:04:17] Found parallel - /usr/local/bin/parallel
[05:04:17] Found freebayes - /usr/local/bin/freebayes
[05:04:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:17] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:17] Found gzip - /bin/gzip
[05:04:17] Found vt - /usr/local/bin/vt
[05:04:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:06:46] This is snippy 4.6.0Show full stderr[05:06:46] This is snippy 4.6.0
[05:06:46] Written by Torsten Seemann
[05:06:46] Obtained from https://github.com/tseemann/snippy
[05:06:46] Detected operating system: linux
[05:06:46] Enabling bundled linux tools.
[05:06:46] Found bwa - /usr/local/bin/bwa
[05:06:46] Found bcftools - /usr/local/bin/bcftools
[05:06:46] Found samtools - /usr/local/bin/samtools
[05:06:46] Found java - /usr/local/bin/java
[05:06:46] Found snpEff - /usr/local/bin/snpEff
[05:06:46] Found samclip - /usr/local/bin/samclip
[05:06:46] Found seqtk - /usr/local/bin/seqtk
[05:06:46] Found parallel - /usr/local/bin/parallel
[05:06:46] Found freebayes - /usr/local/bin/freebayes
[05:06:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:06:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:06:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:06:46] Found vcfuniq - /usr/local/bin/vcfuniq
[05:06:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:06:46] Found gzip - /bin/gzip
[05:06:46] Found vt - /usr/local/bin/vt
[05:06:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:06:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:06:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:06:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:06:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:06:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:06:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:06:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:04:20] This is snippy 4.6.0Show full stderr[05:04:20] This is snippy 4.6.0
[05:04:20] Written by Torsten Seemann
[05:04:20] Obtained from https://github.com/tseemann/snippy
[05:04:20] Detected operating system: linux
[05:04:20] Enabling bundled linux tools.
[05:04:20] Found bwa - /usr/local/bin/bwa
[05:04:20] Found bcftools - /usr/local/bin/bcftools
[05:04:20] Found samtools - /usr/local/bin/samtools
[05:04:20] Found java - /usr/local/bin/java
[05:04:20] Found snpEff - /usr/local/bin/snpEff
[05:04:20] Found samclip - /usr/local/bin/samclip
[05:04:20] Found seqtk - /usr/local/bin/seqtk
[05:04:20] Found parallel - /usr/local/bin/parallel
[05:04:20] Found freebayes - /usr/local/bin/freebayes
[05:04:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:20] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:20] Found gzip - /bin/gzip
[05:04:20] Found vt - /usr/local/bin/vt
[05:04:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:04:35] This is snippy 4.6.0Show full stderr[05:04:35] This is snippy 4.6.0
[05:04:35] Written by Torsten Seemann
[05:04:35] Obtained from https://github.com/tseemann/snippy
[05:04:35] Detected operating system: linux
[05:04:35] Enabling bundled linux tools.
[05:04:35] Found bwa - /usr/local/bin/bwa
[05:04:35] Found bcftools - /usr/local/bin/bcftools
[05:04:35] Found samtools - /usr/local/bin/samtools
[05:04:35] Found java - /usr/local/bin/java
[05:04:35] Found snpEff - /usr/local/bin/snpEff
[05:04:35] Found samclip - /usr/local/bin/samclip
[05:04:35] Found seqtk - /usr/local/bin/seqtk
[05:04:35] Found parallel - /usr/local/bin/parallel
[05:04:35] Found freebayes - /usr/local/bin/freebayes
[05:04:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:35] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:35] Found gzip - /bin/gzip
[05:04:35] Found vt - /usr/local/bin/vt
[05:04:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:04:47] This is snippy 4.6.0Show full stderr[05:04:47] This is snippy 4.6.0
[05:04:47] Written by Torsten Seemann
[05:04:47] Obtained from https://github.com/tseemann/snippy
[05:04:47] Detected operating system: linux
[05:04:47] Enabling bundled linux tools.
[05:04:47] Found bwa - /usr/local/bin/bwa
[05:04:47] Found bcftools - /usr/local/bin/bcftools
[05:04:47] Found samtools - /usr/local/bin/samtools
[05:04:47] Found java - /usr/local/bin/java
[05:04:47] Found snpEff - /usr/local/bin/snpEff
[05:04:47] Found samclip - /usr/local/bin/samclip
[05:04:47] Found seqtk - /usr/local/bin/seqtk
[05:04:47] Found parallel - /usr/local/bin/parallel
[05:04:47] Found freebayes - /usr/local/bin/freebayes
[05:04:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:47] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:47] Found gzip - /bin/gzip
[05:04:47] Found vt - /usr/local/bin/vt
[05:04:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:07:21] This is snippy 4.6.0Show full stderr[05:07:21] This is snippy 4.6.0
[05:07:21] Written by Torsten Seemann
[05:07:21] Obtained from https://github.com/tseemann/snippy
[05:07:21] Detected operating system: linux
[05:07:21] Enabling bundled linux tools.
[05:07:21] Found bwa - /usr/local/bin/bwa
[05:07:21] Found bcftools - /usr/local/bin/bcftools
[05:07:21] Found samtools - /usr/local/bin/samtools
[05:07:21] Found java - /usr/local/bin/java
[05:07:21] Found snpEff - /usr/local/bin/snpEff
[05:07:21] Found samclip - /usr/local/bin/samclip
[05:07:21] Found seqtk - /usr/local/bin/seqtk
[05:07:21] Found parallel - /usr/local/bin/parallel
[05:07:21] Found freebayes - /usr/local/bin/freebayes
[05:07:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:21] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:21] Found gzip - /bin/gzip
[05:07:21] Found vt - /usr/local/bin/vt
[05:07:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:07:30] This is snippy 4.6.0Show full stderr[05:07:30] This is snippy 4.6.0
[05:07:30] Written by Torsten Seemann
[05:07:30] Obtained from https://github.com/tseemann/snippy
[05:07:30] Detected operating system: linux
[05:07:30] Enabling bundled linux tools.
[05:07:30] Found bwa - /usr/local/bin/bwa
[05:07:30] Found bcftools - /usr/local/bin/bcftools
[05:07:30] Found samtools - /usr/local/bin/samtools
[05:07:30] Found java - /usr/local/bin/java
[05:07:30] Found snpEff - /usr/local/bin/snpEff
[05:07:30] Found samclip - /usr/local/bin/samclip
[05:07:30] Found seqtk - /usr/local/bin/seqtk
[05:07:30] Found parallel - /usr/local/bin/parallel
[05:07:30] Found freebayes - /usr/local/bin/freebayes
[05:07:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:30] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:30] Found gzip - /bin/gzip
[05:07:30] Found vt - /usr/local/bin/vt
[05:07:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:07:36] This is snippy 4.6.0Show full stderr[05:07:36] This is snippy 4.6.0
[05:07:36] Written by Torsten Seemann
[05:07:36] Obtained from https://github.com/tseemann/snippy
[05:07:36] Detected operating system: linux
[05:07:36] Enabling bundled linux tools.
[05:07:36] Found bwa - /usr/local/bin/bwa
[05:07:36] Found bcftools - /usr/local/bin/bcftools
[05:07:36] Found samtools - /usr/local/bin/samtools
[05:07:36] Found java - /usr/local/bin/java
[05:07:36] Found snpEff - /usr/local/bin/snpEff
[05:07:36] Found samclip - /usr/local/bin/samclip
[05:07:36] Found seqtk - /usr/local/bin/seqtk
[05:07:36] Found parallel - /usr/local/bin/parallel
[05:07:36] Found freebayes - /usr/local/bin/freebayes
[05:07:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:36] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:36] Found gzip - /bin/gzip
[05:07:36] Found vt - /usr/local/bin/vt
[05:07:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:07:06] This is snippy 4.6.0Show full stderr[05:07:06] This is snippy 4.6.0
[05:07:06] Written by Torsten Seemann
[05:07:06] Obtained from https://github.com/tseemann/snippy
[05:07:06] Detected operating system: linux
[05:07:06] Enabling bundled linux tools.
[05:07:06] Found bwa - /usr/local/bin/bwa
[05:07:06] Found bcftools - /usr/local/bin/bcftools
[05:07:06] Found samtools - /usr/local/bin/samtools
[05:07:06] Found java - /usr/local/bin/java
[05:07:06] Found snpEff - /usr/local/bin/snpEff
[05:07:06] Found samclip - /usr/local/bin/samclip
[05:07:06] Found seqtk - /usr/local/bin/seqtk
[05:07:06] Found parallel - /usr/local/bin/parallel
[05:07:06] Found freebayes - /usr/local/bin/freebayes
[05:07:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:06] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:06] Found gzip - /bin/gzip
[05:07:06] Found vt - /usr/local/bin/vt
[05:07:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:07:51] This is snippy 4.6.0Show full stderr[05:07:51] This is snippy 4.6.0
[05:07:51] Written by Torsten Seemann
[05:07:51] Obtained from https://github.com/tseemann/snippy
[05:07:51] Detected operating system: linux
[05:07:51] Enabling bundled linux tools.
[05:07:51] Found bwa - /usr/local/bin/bwa
[05:07:51] Found bcftools - /usr/local/bin/bcftools
[05:07:51] Found samtools - /usr/local/bin/samtools
[05:07:51] Found java - /usr/local/bin/java
[05:07:51] Found snpEff - /usr/local/bin/snpEff
[05:07:51] Found samclip - /usr/local/bin/samclip
[05:07:51] Found seqtk - /usr/local/bin/seqtk
[05:07:51] Found parallel - /usr/local/bin/parallel
[05:07:51] Found freebayes - /usr/local/bin/freebayes
[05:07:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:51] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:51] Found gzip - /bin/gzip
[05:07:51] Found vt - /usr/local/bin/vt
[05:07:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:07:57] This is snippy 4.6.0Show full stderr[05:07:57] This is snippy 4.6.0
[05:07:57] Written by Torsten Seemann
[05:07:57] Obtained from https://github.com/tseemann/snippy
[05:07:57] Detected operating system: linux
[05:07:57] Enabling bundled linux tools.
[05:07:57] Found bwa - /usr/local/bin/bwa
[05:07:57] Found bcftools - /usr/local/bin/bcftools
[05:07:57] Found samtools - /usr/local/bin/samtools
[05:07:57] Found java - /usr/local/bin/java
[05:07:57] Found snpEff - /usr/local/bin/snpEff
[05:07:57] Found samclip - /usr/local/bin/samclip
[05:07:57] Found seqtk - /usr/local/bin/seqtk
[05:07:57] Found parallel - /usr/local/bin/parallel
[05:07:57] Found freebayes - /usr/local/bin/freebayes
[05:07:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:57] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:57] Found gzip - /bin/gzip
[05:07:57] Found vt - /usr/local/bin/vt
[05:07:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:08:12] This is snippy 4.6.0Show full stderr[05:08:12] This is snippy 4.6.0
[05:08:12] Written by Torsten Seemann
[05:08:12] Obtained from https://github.com/tseemann/snippy
[05:08:12] Detected operating system: linux
[05:08:12] Enabling bundled linux tools.
[05:08:12] Found bwa - /usr/local/bin/bwa
[05:08:12] Found bcftools - /usr/local/bin/bcftools
[05:08:12] Found samtools - /usr/local/bin/samtools
[05:08:12] Found java - /usr/local/bin/java
[05:08:12] Found snpEff - /usr/local/bin/snpEff
[05:08:12] Found samclip - /usr/local/bin/samclip
[05:08:12] Found seqtk - /usr/local/bin/seqtk
[05:08:12] Found parallel - /usr/local/bin/parallel
[05:08:12] Found freebayes - /usr/local/bin/freebayes
[05:08:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:12] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:12] Found gzip - /bin/gzip
[05:08:12] Found vt - /usr/local/bin/vt
[05:08:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:08:39] This is snippy 4.6.0Show full stderr[05:08:39] This is snippy 4.6.0
[05:08:39] Written by Torsten Seemann
[05:08:39] Obtained from https://github.com/tseemann/snippy
[05:08:39] Detected operating system: linux
[05:08:39] Enabling bundled linux tools.
[05:08:39] Found bwa - /usr/local/bin/bwa
[05:08:39] Found bcftools - /usr/local/bin/bcftools
[05:08:39] Found samtools - /usr/local/bin/samtools
[05:08:39] Found java - /usr/local/bin/java
[05:08:39] Found snpEff - /usr/local/bin/snpEff
[05:08:39] Found samclip - /usr/local/bin/samclip
[05:08:39] Found seqtk - /usr/local/bin/seqtk
[05:08:39] Found parallel - /usr/local/bin/parallel
[05:08:39] Found freebayes - /usr/local/bin/freebayes
[05:08:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:39] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:39] Found gzip - /bin/gzip
[05:08:39] Found vt - /usr/local/bin/vt
[05:08:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:09:09] This is snippy 4.6.0Show full stderr[05:09:09] This is snippy 4.6.0
[05:09:09] Written by Torsten Seemann
[05:09:09] Obtained from https://github.com/tseemann/snippy
[05:09:09] Detected operating system: linux
[05:09:09] Enabling bundled linux tools.
[05:09:09] Found bwa - /usr/local/bin/bwa
[05:09:09] Found bcftools - /usr/local/bin/bcftools
[05:09:09] Found samtools - /usr/local/bin/samtools
[05:09:09] Found java - /usr/local/bin/java
[05:09:09] Found snpEff - /usr/local/bin/snpEff
[05:09:09] Found samclip - /usr/local/bin/samclip
[05:09:09] Found seqtk - /usr/local/bin/seqtk
[05:09:09] Found parallel - /usr/local/bin/parallel
[05:09:09] Found freebayes - /usr/local/bin/freebayes
[05:09:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:09] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:09] Found gzip - /bin/gzip
[05:09:09] Found vt - /usr/local/bin/vt
[05:09:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:09:24] This is snippy 4.6.0Show full stderr[05:09:24] This is snippy 4.6.0
[05:09:24] Written by Torsten Seemann
[05:09:24] Obtained from https://github.com/tseemann/snippy
[05:09:24] Detected operating system: linux
[05:09:24] Enabling bundled linux tools.
[05:09:24] Found bwa - /usr/local/bin/bwa
[05:09:24] Found bcftools - /usr/local/bin/bcftools
[05:09:24] Found samtools - /usr/local/bin/samtools
[05:09:24] Found java - /usr/local/bin/java
[05:09:24] Found snpEff - /usr/local/bin/snpEff
[05:09:24] Found samclip - /usr/local/bin/samclip
[05:09:24] Found seqtk - /usr/local/bin/seqtk
[05:09:24] Found parallel - /usr/local/bin/parallel
[05:09:24] Found freebayes - /usr/local/bin/freebayes
[05:09:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:24] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:24] Found gzip - /bin/gzip
[05:09:24] Found vt - /usr/local/bin/vt
[05:09:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:09:39] This is snippy 4.6.0Show full stderr[05:09:39] This is snippy 4.6.0
[05:09:39] Written by Torsten Seemann
[05:09:39] Obtained from https://github.com/tseemann/snippy
[05:09:39] Detected operating system: linux
[05:09:39] Enabling bundled linux tools.
[05:09:39] Found bwa - /usr/local/bin/bwa
[05:09:39] Found bcftools - /usr/local/bin/bcftools
[05:09:39] Found samtools - /usr/local/bin/samtools
[05:09:39] Found java - /usr/local/bin/java
[05:09:39] Found snpEff - /usr/local/bin/snpEff
[05:09:39] Found samclip - /usr/local/bin/samclip
[05:09:39] Found seqtk - /usr/local/bin/seqtk
[05:09:39] Found parallel - /usr/local/bin/parallel
[05:09:39] Found freebayes - /usr/local/bin/freebayes
[05:09:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:39] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:39] Found gzip - /bin/gzip
[05:09:39] Found vt - /usr/local/bin/vt
[05:09:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:03:02] This is snippy 4.6.0Show full stderr[05:03:02] This is snippy 4.6.0
[05:03:02] Written by Torsten Seemann
[05:03:02] Obtained from https://github.com/tseemann/snippy
[05:03:02] Detected operating system: linux
[05:03:02] Enabling bundled linux tools.
[05:03:02] Found bwa - /usr/local/bin/bwa
[05:03:02] Found bcftools - /usr/local/bin/bcftools
[05:03:02] Found samtools - /usr/local/bin/samtools
[05:03:02] Found java - /usr/local/bin/java
[05:03:02] Found snpEff - /usr/local/bin/snpEff
[05:03:02] Found samclip - /usr/local/bin/samclip
[05:03:03] Found seqtk - /usr/local/bin/seqtk
[05:03:03] Found parallel - /usr/local/bin/parallel
[05:03:03] Found freebayes - /usr/local/bin/freebayes
[05:03:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:03] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:03] Found gzip - /bin/gzip
[05:03:03] Found vt - /usr/local/bin/vt
[05:03:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:04:50] This is snippy 4.6.0Show full stderr[05:04:50] This is snippy 4.6.0
[05:04:50] Written by Torsten Seemann
[05:04:50] Obtained from https://github.com/tseemann/snippy
[05:04:50] Detected operating system: linux
[05:04:50] Enabling bundled linux tools.
[05:04:50] Found bwa - /usr/local/bin/bwa
[05:04:50] Found bcftools - /usr/local/bin/bcftools
[05:04:50] Found samtools - /usr/local/bin/samtools
[05:04:50] Found java - /usr/local/bin/java
[05:04:50] Found snpEff - /usr/local/bin/snpEff
[05:04:50] Found samclip - /usr/local/bin/samclip
[05:04:50] Found seqtk - /usr/local/bin/seqtk
[05:04:50] Found parallel - /usr/local/bin/parallel
[05:04:50] Found freebayes - /usr/local/bin/freebayes
[05:04:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:50] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:50] Found gzip - /bin/gzip
[05:04:50] Found vt - /usr/local/bin/vt
[05:04:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:09:48] This is snippy 4.6.0Show full stderr[05:09:48] This is snippy 4.6.0
[05:09:48] Written by Torsten Seemann
[05:09:48] Obtained from https://github.com/tseemann/snippy
[05:09:48] Detected operating system: linux
[05:09:48] Enabling bundled linux tools.
[05:09:48] Found bwa - /usr/local/bin/bwa
[05:09:48] Found bcftools - /usr/local/bin/bcftools
[05:09:48] Found samtools - /usr/local/bin/samtools
[05:09:48] Found java - /usr/local/bin/java
[05:09:48] Found snpEff - /usr/local/bin/snpEff
[05:09:48] Found samclip - /usr/local/bin/samclip
[05:09:48] Found seqtk - /usr/local/bin/seqtk
[05:09:48] Found parallel - /usr/local/bin/parallel
[05:09:48] Found freebayes - /usr/local/bin/freebayes
[05:09:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:48] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:48] Found gzip - /bin/gzip
[05:09:48] Found vt - /usr/local/bin/vt
[05:09:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:09:54] This is snippy 4.6.0Show full stderr[05:09:54] This is snippy 4.6.0
[05:09:54] Written by Torsten Seemann
[05:09:54] Obtained from https://github.com/tseemann/snippy
[05:09:54] Detected operating system: linux
[05:09:54] Enabling bundled linux tools.
[05:09:54] Found bwa - /usr/local/bin/bwa
[05:09:54] Found bcftools - /usr/local/bin/bcftools
[05:09:54] Found samtools - /usr/local/bin/samtools
[05:09:54] Found java - /usr/local/bin/java
[05:09:54] Found snpEff - /usr/local/bin/snpEff
[05:09:54] Found samclip - /usr/local/bin/samclip
[05:09:54] Found seqtk - /usr/local/bin/seqtk
[05:09:54] Found parallel - /usr/local/bin/parallel
[05:09:54] Found freebayes - /usr/local/bin/freebayes
[05:09:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:54] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:54] Found gzip - /bin/gzip
[05:09:54] Found vt - /usr/local/bin/vt
[05:09:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:10:09] This is snippy 4.6.0Show full stderr[05:10:09] This is snippy 4.6.0
[05:10:09] Written by Torsten Seemann
[05:10:09] Obtained from https://github.com/tseemann/snippy
[05:10:09] Detected operating system: linux
[05:10:09] Enabling bundled linux tools.
[05:10:09] Found bwa - /usr/local/bin/bwa
[05:10:09] Found bcftools - /usr/local/bin/bcftools
[05:10:09] Found samtools - /usr/local/bin/samtools
[05:10:09] Found java - /usr/local/bin/java
[05:10:09] Found snpEff - /usr/local/bin/snpEff
[05:10:09] Found samclip - /usr/local/bin/samclip
[05:10:09] Found seqtk - /usr/local/bin/seqtk
[05:10:09] Found parallel - /usr/local/bin/parallel
[05:10:09] Found freebayes - /usr/local/bin/freebayes
[05:10:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:09] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:09] Found gzip - /bin/gzip
[05:10:09] Found vt - /usr/local/bin/vt
[05:10:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:10:27] This is snippy 4.6.0Show full stderr[05:10:27] This is snippy 4.6.0
[05:10:27] Written by Torsten Seemann
[05:10:27] Obtained from https://github.com/tseemann/snippy
[05:10:27] Detected operating system: linux
[05:10:27] Enabling bundled linux tools.
[05:10:27] Found bwa - /usr/local/bin/bwa
[05:10:27] Found bcftools - /usr/local/bin/bcftools
[05:10:27] Found samtools - /usr/local/bin/samtools
[05:10:27] Found java - /usr/local/bin/java
[05:10:27] Found snpEff - /usr/local/bin/snpEff
[05:10:27] Found samclip - /usr/local/bin/samclip
[05:10:27] Found seqtk - /usr/local/bin/seqtk
[05:10:27] Found parallel - /usr/local/bin/parallel
[05:10:27] Found freebayes - /usr/local/bin/freebayes
[05:10:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:27] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:27] Found gzip - /bin/gzip
[05:10:27] Found vt - /usr/local/bin/vt
[05:10:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:05:03] This is snippy 4.6.0Show full stderr[05:05:03] This is snippy 4.6.0
[05:05:03] Written by Torsten Seemann
[05:05:03] Obtained from https://github.com/tseemann/snippy
[05:05:03] Detected operating system: linux
[05:05:03] Enabling bundled linux tools.
[05:05:03] Found bwa - /usr/local/bin/bwa
[05:05:03] Found bcftools - /usr/local/bin/bcftools
[05:05:03] Found samtools - /usr/local/bin/samtools
[05:05:03] Found java - /usr/local/bin/java
[05:05:03] Found snpEff - /usr/local/bin/snpEff
[05:05:03] Found samclip - /usr/local/bin/samclip
[05:05:03] Found seqtk - /usr/local/bin/seqtk
[05:05:03] Found parallel - /usr/local/bin/parallel
[05:05:03] Found freebayes - /usr/local/bin/freebayes
[05:05:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:03] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:03] Found gzip - /bin/gzip
[05:05:03] Found vt - /usr/local/bin/vt
[05:05:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:05:39] This is snippy 4.6.0Show full stderr[05:05:39] This is snippy 4.6.0
[05:05:39] Written by Torsten Seemann
[05:05:39] Obtained from https://github.com/tseemann/snippy
[05:05:39] Detected operating system: linux
[05:05:39] Enabling bundled linux tools.
[05:05:39] Found bwa - /usr/local/bin/bwa
[05:05:39] Found bcftools - /usr/local/bin/bcftools
[05:05:39] Found samtools - /usr/local/bin/samtools
[05:05:39] Found java - /usr/local/bin/java
[05:05:39] Found snpEff - /usr/local/bin/snpEff
[05:05:39] Found samclip - /usr/local/bin/samclip
[05:05:39] Found seqtk - /usr/local/bin/seqtk
[05:05:39] Found parallel - /usr/local/bin/parallel
[05:05:39] Found freebayes - /usr/local/bin/freebayes
[05:05:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:39] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:39] Found gzip - /bin/gzip
[05:05:39] Found vt - /usr/local/bin/vt
[05:05:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:06:14] This is snippy 4.6.0Show full stderr[05:06:14] This is snippy 4.6.0
[05:06:14] Written by Torsten Seemann
[05:06:14] Obtained from https://github.com/tseemann/snippy
[05:06:14] Detected operating system: linux
[05:06:14] Enabling bundled linux tools.
[05:06:14] Found bwa - /usr/local/bin/bwa
[05:06:14] Found bcftools - /usr/local/bin/bcftools
[05:06:14] Found samtools - /usr/local/bin/samtools
[05:06:14] Found java - /usr/local/bin/java
[05:06:14] Found snpEff - /usr/local/bin/snpEff
[05:06:14] Found samclip - /usr/local/bin/samclip
[05:06:14] Found seqtk - /usr/local/bin/seqtk
[05:06:14] Found parallel - /usr/local/bin/parallel
[05:06:14] Found freebayes - /usr/local/bin/freebayes
[05:06:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:06:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:06:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:06:14] Found vcfuniq - /usr/local/bin/vcfuniq
[05:06:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:06:14] Found gzip - /bin/gzip
[05:06:14] Found vt - /usr/local/bin/vt
[05:06:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:06:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:06:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:06:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:06:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:06:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:06:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:06:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:06:33] This is snippy 4.6.0Show full stderr[05:06:33] This is snippy 4.6.0
[05:06:33] Written by Torsten Seemann
[05:06:33] Obtained from https://github.com/tseemann/snippy
[05:06:33] Detected operating system: linux
[05:06:33] Enabling bundled linux tools.
[05:06:33] Found bwa - /usr/local/bin/bwa
[05:06:33] Found bcftools - /usr/local/bin/bcftools
[05:06:33] Found samtools - /usr/local/bin/samtools
[05:06:33] Found java - /usr/local/bin/java
[05:06:33] Found snpEff - /usr/local/bin/snpEff
[05:06:33] Found samclip - /usr/local/bin/samclip
[05:06:33] Found seqtk - /usr/local/bin/seqtk
[05:06:33] Found parallel - /usr/local/bin/parallel
[05:06:33] Found freebayes - /usr/local/bin/freebayes
[05:06:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:06:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:06:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:06:33] Found vcfuniq - /usr/local/bin/vcfuniq
[05:06:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:06:33] Found gzip - /bin/gzip
[05:06:33] Found vt - /usr/local/bin/vt
[05:06:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:06:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:06:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:06:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:06:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:06:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:06:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:06:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:10:24] This is snippy 4.6.0Show full stderr[05:10:24] This is snippy 4.6.0
[05:10:24] Written by Torsten Seemann
[05:10:24] Obtained from https://github.com/tseemann/snippy
[05:10:24] Detected operating system: linux
[05:10:24] Enabling bundled linux tools.
[05:10:24] Found bwa - /usr/local/bin/bwa
[05:10:24] Found bcftools - /usr/local/bin/bcftools
[05:10:24] Found samtools - /usr/local/bin/samtools
[05:10:24] Found java - /usr/local/bin/java
[05:10:24] Found snpEff - /usr/local/bin/snpEff
[05:10:24] Found samclip - /usr/local/bin/samclip
[05:10:24] Found seqtk - /usr/local/bin/seqtk
[05:10:24] Found parallel - /usr/local/bin/parallel
[05:10:24] Found freebayes - /usr/local/bin/freebayes
[05:10:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:24] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:24] Found gzip - /bin/gzip
[05:10:24] Found vt - /usr/local/bin/vt
[05:10:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:08:09] This is snippy 4.6.0Show full stderr[05:08:09] This is snippy 4.6.0
[05:08:09] Written by Torsten Seemann
[05:08:09] Obtained from https://github.com/tseemann/snippy
[05:08:09] Detected operating system: linux
[05:08:09] Enabling bundled linux tools.
[05:08:09] Found bwa - /usr/local/bin/bwa
[05:08:09] Found bcftools - /usr/local/bin/bcftools
[05:08:09] Found samtools - /usr/local/bin/samtools
[05:08:09] Found java - /usr/local/bin/java
[05:08:09] Found snpEff - /usr/local/bin/snpEff
[05:08:09] Found samclip - /usr/local/bin/samclip
[05:08:09] Found seqtk - /usr/local/bin/seqtk
[05:08:09] Found parallel - /usr/local/bin/parallel
[05:08:09] Found freebayes - /usr/local/bin/freebayes
[05:08:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:09] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:09] Found gzip - /bin/gzip
[05:08:09] Found vt - /usr/local/bin/vt
[05:08:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:08:42] This is snippy 4.6.0Show full stderr[05:08:42] This is snippy 4.6.0
[05:08:42] Written by Torsten Seemann
[05:08:42] Obtained from https://github.com/tseemann/snippy
[05:08:42] Detected operating system: linux
[05:08:42] Enabling bundled linux tools.
[05:08:42] Found bwa - /usr/local/bin/bwa
[05:08:42] Found bcftools - /usr/local/bin/bcftools
[05:08:42] Found samtools - /usr/local/bin/samtools
[05:08:42] Found java - /usr/local/bin/java
[05:08:42] Found snpEff - /usr/local/bin/snpEff
[05:08:42] Found samclip - /usr/local/bin/samclip
[05:08:42] Found seqtk - /usr/local/bin/seqtk
[05:08:42] Found parallel - /usr/local/bin/parallel
[05:08:42] Found freebayes - /usr/local/bin/freebayes
[05:08:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:42] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:42] Found gzip - /bin/gzip
[05:08:42] Found vt - /usr/local/bin/vt
[05:08:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:11:30] This is snippy 4.6.0Show full stderr[05:11:30] This is snippy 4.6.0
[05:11:30] Written by Torsten Seemann
[05:11:30] Obtained from https://github.com/tseemann/snippy
[05:11:30] Detected operating system: linux
[05:11:30] Enabling bundled linux tools.
[05:11:30] Found bwa - /usr/local/bin/bwa
[05:11:30] Found bcftools - /usr/local/bin/bcftools
[05:11:30] Found samtools - /usr/local/bin/samtools
[05:11:30] Found java - /usr/local/bin/java
[05:11:30] Found snpEff - /usr/local/bin/snpEff
[05:11:30] Found samclip - /usr/local/bin/samclip
[05:11:30] Found seqtk - /usr/local/bin/seqtk
[05:11:30] Found parallel - /usr/local/bin/parallel
[05:11:30] Found freebayes - /usr/local/bin/freebayes
[05:11:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:11:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:11:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:11:30] Found vcfuniq - /usr/local/bin/vcfuniq
[05:11:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:11:30] Found gzip - /bin/gzip
[05:11:30] Found vt - /usr/local/bin/vt
[05:11:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:11:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:11:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:11:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:11:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:11:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:11:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:11:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:11:42] This is snippy 4.6.0Show full stderr[05:11:42] This is snippy 4.6.0
[05:11:42] Written by Torsten Seemann
[05:11:42] Obtained from https://github.com/tseemann/snippy
[05:11:42] Detected operating system: linux
[05:11:42] Enabling bundled linux tools.
[05:11:42] Found bwa - /usr/local/bin/bwa
[05:11:42] Found bcftools - /usr/local/bin/bcftools
[05:11:42] Found samtools - /usr/local/bin/samtools
[05:11:42] Found java - /usr/local/bin/java
[05:11:42] Found snpEff - /usr/local/bin/snpEff
[05:11:42] Found samclip - /usr/local/bin/samclip
[05:11:42] Found seqtk - /usr/local/bin/seqtk
[05:11:42] Found parallel - /usr/local/bin/parallel
[05:11:42] Found freebayes - /usr/local/bin/freebayes
[05:11:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:11:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:11:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:11:42] Found vcfuniq - /usr/local/bin/vcfuniq
[05:11:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:11:42] Found gzip - /bin/gzip
[05:11:42] Found vt - /usr/local/bin/vt
[05:11:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:11:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:11:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:11:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:11:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:11:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:11:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:11:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:08:57] This is snippy 4.6.0Show full stderr[05:08:57] This is snippy 4.6.0
[05:08:57] Written by Torsten Seemann
[05:08:57] Obtained from https://github.com/tseemann/snippy
[05:08:57] Detected operating system: linux
[05:08:57] Enabling bundled linux tools.
[05:08:57] Found bwa - /usr/local/bin/bwa
[05:08:57] Found bcftools - /usr/local/bin/bcftools
[05:08:57] Found samtools - /usr/local/bin/samtools
[05:08:57] Found java - /usr/local/bin/java
[05:08:57] Found snpEff - /usr/local/bin/snpEff
[05:08:57] Found samclip - /usr/local/bin/samclip
[05:08:57] Found seqtk - /usr/local/bin/seqtk
[05:08:57] Found parallel - /usr/local/bin/parallel
[05:08:57] Found freebayes - /usr/local/bin/freebayes
[05:08:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:57] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:57] Found gzip - /bin/gzip
[05:08:57] Found vt - /usr/local/bin/vt
[05:08:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:39:33] This is snippy 4.6.0Show full stderr[03:39:33] This is snippy 4.6.0
[03:39:33] Written by Torsten Seemann
[03:39:33] Obtained from https://github.com/tseemann/snippy
[03:39:33] Detected operating system: linux
[03:39:33] Enabling bundled linux tools.
[03:39:33] Found bwa - /usr/local/bin/bwa
[03:39:33] Found bcftools - /usr/local/bin/bcftools
[03:39:33] Found samtools - /usr/local/bin/samtools
[03:39:33] Found java - /usr/local/bin/java
[03:39:33] Found snpEff - /usr/local/bin/snpEff
[03:39:33] Found samclip - /usr/local/bin/samclip
[03:39:33] Found seqtk - /usr/local/bin/seqtk
[03:39:33] Found parallel - /usr/local/bin/parallel
[03:39:33] Found freebayes - /usr/local/bin/freebayes
[03:39:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:39:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:39:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:39:33] Found vcfuniq - /usr/local/bin/vcfuniq
[03:39:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:39:33] Found gzip - /bin/gzip
[03:39:33] Found vt - /usr/local/bin/vt
[03:39:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:39:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:39:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:39:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:39:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:39:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:39:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:39:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:40:34] This is snippy 4.6.0Show full stderr[03:40:34] This is snippy 4.6.0
[03:40:34] Written by Torsten Seemann
[03:40:34] Obtained from https://github.com/tseemann/snippy
[03:40:34] Detected operating system: linux
[03:40:34] Enabling bundled linux tools.
[03:40:34] Found bwa - /usr/local/bin/bwa
[03:40:34] Found bcftools - /usr/local/bin/bcftools
[03:40:34] Found samtools - /usr/local/bin/samtools
[03:40:34] Found java - /usr/local/bin/java
[03:40:34] Found snpEff - /usr/local/bin/snpEff
[03:40:34] Found samclip - /usr/local/bin/samclip
[03:40:34] Found seqtk - /usr/local/bin/seqtk
[03:40:34] Found parallel - /usr/local/bin/parallel
[03:40:34] Found freebayes - /usr/local/bin/freebayes
[03:40:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:34] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:34] Found gzip - /bin/gzip
[03:40:34] Found vt - /usr/local/bin/vt
[03:40:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:41:27] This is snippy 4.6.0Show full stderr[03:41:27] This is snippy 4.6.0
[03:41:27] Written by Torsten Seemann
[03:41:27] Obtained from https://github.com/tseemann/snippy
[03:41:27] Detected operating system: linux
[03:41:27] Enabling bundled linux tools.
[03:41:27] Found bwa - /usr/local/bin/bwa
[03:41:27] Found bcftools - /usr/local/bin/bcftools
[03:41:27] Found samtools - /usr/local/bin/samtools
[03:41:27] Found java - /usr/local/bin/java
[03:41:27] Found snpEff - /usr/local/bin/snpEff
[03:41:27] Found samclip - /usr/local/bin/samclip
[03:41:27] Found seqtk - /usr/local/bin/seqtk
[03:41:27] Found parallel - /usr/local/bin/parallel
[03:41:27] Found freebayes - /usr/local/bin/freebayes
[03:41:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:41:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:41:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:41:27] Found vcfuniq - /usr/local/bin/vcfuniq
[03:41:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:41:27] Found gzip - /bin/gzip
[03:41:27] Found vt - /usr/local/bin/vt
[03:41:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:41:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:41:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:41:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:41:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:41:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:41:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:41:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:40:49] This is snippy 4.6.0Show full stderr[03:40:49] This is snippy 4.6.0
[03:40:49] Written by Torsten Seemann
[03:40:49] Obtained from https://github.com/tseemann/snippy
[03:40:49] Detected operating system: linux
[03:40:49] Enabling bundled linux tools.
[03:40:49] Found bwa - /usr/local/bin/bwa
[03:40:49] Found bcftools - /usr/local/bin/bcftools
[03:40:49] Found samtools - /usr/local/bin/samtools
[03:40:49] Found java - /usr/local/bin/java
[03:40:49] Found snpEff - /usr/local/bin/snpEff
[03:40:49] Found samclip - /usr/local/bin/samclip
[03:40:49] Found seqtk - /usr/local/bin/seqtk
[03:40:49] Found parallel - /usr/local/bin/parallel
[03:40:49] Found freebayes - /usr/local/bin/freebayes
[03:40:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:49] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:49] Found gzip - /bin/gzip
[03:40:49] Found vt - /usr/local/bin/vt
[03:40:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:41:00] This is snippy 4.6.0Show full stderr[03:41:00] This is snippy 4.6.0
[03:41:00] Written by Torsten Seemann
[03:41:00] Obtained from https://github.com/tseemann/snippy
[03:41:00] Detected operating system: linux
[03:41:00] Enabling bundled linux tools.
[03:41:00] Found bwa - /usr/local/bin/bwa
[03:41:00] Found bcftools - /usr/local/bin/bcftools
[03:41:00] Found samtools - /usr/local/bin/samtools
[03:41:00] Found java - /usr/local/bin/java
[03:41:00] Found snpEff - /usr/local/bin/snpEff
[03:41:00] Found samclip - /usr/local/bin/samclip
[03:41:00] Found seqtk - /usr/local/bin/seqtk
[03:41:00] Found parallel - /usr/local/bin/parallel
[03:41:00] Found freebayes - /usr/local/bin/freebayes
[03:41:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:41:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:41:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:41:00] Found vcfuniq - /usr/local/bin/vcfuniq
[03:41:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:41:00] Found gzip - /bin/gzip
[03:41:00] Found vt - /usr/local/bin/vt
[03:41:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:41:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:41:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:41:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:41:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:41:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:41:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:41:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:42:00] This is snippy 4.6.0Show full stderr[03:42:00] This is snippy 4.6.0
[03:42:00] Written by Torsten Seemann
[03:42:00] Obtained from https://github.com/tseemann/snippy
[03:42:00] Detected operating system: linux
[03:42:00] Enabling bundled linux tools.
[03:42:00] Found bwa - /usr/local/bin/bwa
[03:42:00] Found bcftools - /usr/local/bin/bcftools
[03:42:00] Found samtools - /usr/local/bin/samtools
[03:42:00] Found java - /usr/local/bin/java
[03:42:00] Found snpEff - /usr/local/bin/snpEff
[03:42:00] Found samclip - /usr/local/bin/samclip
[03:42:00] Found seqtk - /usr/local/bin/seqtk
[03:42:00] Found parallel - /usr/local/bin/parallel
[03:42:00] Found freebayes - /usr/local/bin/freebayes
[03:42:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:00] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:00] Found gzip - /bin/gzip
[03:42:00] Found vt - /usr/local/bin/vt
[03:42:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:42:16] This is snippy 4.6.0Show full stderr[03:42:16] This is snippy 4.6.0
[03:42:16] Written by Torsten Seemann
[03:42:16] Obtained from https://github.com/tseemann/snippy
[03:42:16] Detected operating system: linux
[03:42:16] Enabling bundled linux tools.
[03:42:16] Found bwa - /usr/local/bin/bwa
[03:42:16] Found bcftools - /usr/local/bin/bcftools
[03:42:16] Found samtools - /usr/local/bin/samtools
[03:42:16] Found java - /usr/local/bin/java
[03:42:16] Found snpEff - /usr/local/bin/snpEff
[03:42:16] Found samclip - /usr/local/bin/samclip
[03:42:16] Found seqtk - /usr/local/bin/seqtk
[03:42:16] Found parallel - /usr/local/bin/parallel
[03:42:16] Found freebayes - /usr/local/bin/freebayes
[03:42:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:16] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:16] Found gzip - /bin/gzip
[03:42:16] Found vt - /usr/local/bin/vt
[03:42:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:43:10] This is snippy 4.6.0Show full stderr[03:43:10] This is snippy 4.6.0
[03:43:10] Written by Torsten Seemann
[03:43:10] Obtained from https://github.com/tseemann/snippy
[03:43:10] Detected operating system: linux
[03:43:10] Enabling bundled linux tools.
[03:43:10] Found bwa - /usr/local/bin/bwa
[03:43:10] Found bcftools - /usr/local/bin/bcftools
[03:43:10] Found samtools - /usr/local/bin/samtools
[03:43:10] Found java - /usr/local/bin/java
[03:43:10] Found snpEff - /usr/local/bin/snpEff
[03:43:10] Found samclip - /usr/local/bin/samclip
[03:43:10] Found seqtk - /usr/local/bin/seqtk
[03:43:10] Found parallel - /usr/local/bin/parallel
[03:43:10] Found freebayes - /usr/local/bin/freebayes
[03:43:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:10] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:10] Found gzip - /bin/gzip
[03:43:10] Found vt - /usr/local/bin/vt
[03:43:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:43:28] This is snippy 4.6.0Show full stderr[03:43:28] This is snippy 4.6.0
[03:43:28] Written by Torsten Seemann
[03:43:28] Obtained from https://github.com/tseemann/snippy
[03:43:28] Detected operating system: linux
[03:43:28] Enabling bundled linux tools.
[03:43:28] Found bwa - /usr/local/bin/bwa
[03:43:28] Found bcftools - /usr/local/bin/bcftools
[03:43:28] Found samtools - /usr/local/bin/samtools
[03:43:28] Found java - /usr/local/bin/java
[03:43:28] Found snpEff - /usr/local/bin/snpEff
[03:43:28] Found samclip - /usr/local/bin/samclip
[03:43:28] Found seqtk - /usr/local/bin/seqtk
[03:43:28] Found parallel - /usr/local/bin/parallel
[03:43:28] Found freebayes - /usr/local/bin/freebayes
[03:43:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:28] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:28] Found gzip - /bin/gzip
[03:43:28] Found vt - /usr/local/bin/vt
[03:43:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:43:43] This is snippy 4.6.0Show full stderr[03:43:43] This is snippy 4.6.0
[03:43:43] Written by Torsten Seemann
[03:43:43] Obtained from https://github.com/tseemann/snippy
[03:43:43] Detected operating system: linux
[03:43:43] Enabling bundled linux tools.
[03:43:43] Found bwa - /usr/local/bin/bwa
[03:43:43] Found bcftools - /usr/local/bin/bcftools
[03:43:43] Found samtools - /usr/local/bin/samtools
[03:43:43] Found java - /usr/local/bin/java
[03:43:43] Found snpEff - /usr/local/bin/snpEff
[03:43:43] Found samclip - /usr/local/bin/samclip
[03:43:43] Found seqtk - /usr/local/bin/seqtk
[03:43:43] Found parallel - /usr/local/bin/parallel
[03:43:43] Found freebayes - /usr/local/bin/freebayes
[03:43:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:43] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:43] Found gzip - /bin/gzip
[03:43:43] Found vt - /usr/local/bin/vt
[03:43:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:42:10] This is snippy 4.6.0Show full stderr[03:42:10] This is snippy 4.6.0
[03:42:10] Written by Torsten Seemann
[03:42:10] Obtained from https://github.com/tseemann/snippy
[03:42:10] Detected operating system: linux
[03:42:10] Enabling bundled linux tools.
[03:42:10] Found bwa - /usr/local/bin/bwa
[03:42:10] Found bcftools - /usr/local/bin/bcftools
[03:42:10] Found samtools - /usr/local/bin/samtools
[03:42:10] Found java - /usr/local/bin/java
[03:42:10] Found snpEff - /usr/local/bin/snpEff
[03:42:10] Found samclip - /usr/local/bin/samclip
[03:42:10] Found seqtk - /usr/local/bin/seqtk
[03:42:10] Found parallel - /usr/local/bin/parallel
[03:42:10] Found freebayes - /usr/local/bin/freebayes
[03:42:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:10] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:10] Found gzip - /bin/gzip
[03:42:10] Found vt - /usr/local/bin/vt
[03:42:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:43:58] This is snippy 4.6.0Show full stderr[03:43:58] This is snippy 4.6.0
[03:43:58] Written by Torsten Seemann
[03:43:58] Obtained from https://github.com/tseemann/snippy
[03:43:58] Detected operating system: linux
[03:43:58] Enabling bundled linux tools.
[03:43:58] Found bwa - /usr/local/bin/bwa
[03:43:58] Found bcftools - /usr/local/bin/bcftools
[03:43:58] Found samtools - /usr/local/bin/samtools
[03:43:58] Found java - /usr/local/bin/java
[03:43:58] Found snpEff - /usr/local/bin/snpEff
[03:43:58] Found samclip - /usr/local/bin/samclip
[03:43:58] Found seqtk - /usr/local/bin/seqtk
[03:43:58] Found parallel - /usr/local/bin/parallel
[03:43:58] Found freebayes - /usr/local/bin/freebayes
[03:43:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:58] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:58] Found gzip - /bin/gzip
[03:43:58] Found vt - /usr/local/bin/vt
[03:43:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [03:44:13] This is snippy 4.6.0Show full stderr[03:44:13] This is snippy 4.6.0
[03:44:13] Written by Torsten Seemann
[03:44:13] Obtained from https://github.com/tseemann/snippy
[03:44:13] Detected operating system: linux
[03:44:13] Enabling bundled linux tools.
[03:44:13] Found bwa - /usr/local/bin/bwa
[03:44:13] Found bcftools - /usr/local/bin/bcftools
[03:44:13] Found samtools - /usr/local/bin/samtools
[03:44:13] Found java - /usr/local/bin/java
[03:44:13] Found snpEff - /usr/local/bin/snpEff
[03:44:13] Found samclip - /usr/local/bin/samclip
[03:44:13] Found seqtk - /usr/local/bin/seqtk
[03:44:13] Found parallel - /usr/local/bin/parallel
[03:44:13] Found freebayes - /usr/local/bin/freebayes
[03:44:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:44:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:44:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:44:13] Found vcfuniq - /usr/local/bin/vcfuniq
[03:44:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:44:13] Found gzip - /bin/gzip
[03:44:13] Found vt - /usr/local/bin/vt
[03:44:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:44:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:44:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:44:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:44:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:44:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:44:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:44:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:57:56] This is snippy 4.6.0Show full stderr[05:57:56] This is snippy 4.6.0
[05:57:56] Written by Torsten Seemann
[05:57:56] Obtained from https://github.com/tseemann/snippy
[05:57:56] Detected operating system: linux
[05:57:56] Enabling bundled linux tools.
[05:57:56] Found bwa - /usr/local/bin/bwa
[05:57:56] Found bcftools - /usr/local/bin/bcftools
[05:57:56] Found samtools - /usr/local/bin/samtools
[05:57:56] Found java - /usr/local/bin/java
[05:57:56] Found snpEff - /usr/local/bin/snpEff
[05:57:56] Found samclip - /usr/local/bin/samclip
[05:57:56] Found seqtk - /usr/local/bin/seqtk
[05:57:56] Found parallel - /usr/local/bin/parallel
[05:57:56] Found freebayes - /usr/local/bin/freebayes
[05:57:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:57:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:57:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:57:57] Found vcfuniq - /usr/local/bin/vcfuniq
[05:57:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:57:57] Found gzip - /bin/gzip
[05:57:57] Found vt - /usr/local/bin/vt
[05:57:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:57:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:57:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:57:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:57:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:57:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:57:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:57:58] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:57:58] Treating reference as 'fasta' format.
[05:57:58] Will use 1 CPU cores.
[05:57:58] Using read file: /corral4/main/objects/c/5/6/dataset_c562894c-07c6-4167-b0aa-6a642b1bae17.dat
[05:57:58] Creating folder: Resistance_28_fasta
[05:57:58] Changing working directory: Resistance_28_fasta
[05:57:58] Creating reference folder: reference
[05:57:58] Extracting FASTA and GFF from reference.
[05:57:58] Wrote 3 sequences to ref.fa
[05:57:58] Wrote 0 features to ref.gff
[05:57:58] Shredding /corral4/main/objects/c/5/6/dataset_c562894c-07c6-4167-b0aa-6a642b1bae17.dat into pseudo-reads
[05:58:05] Wrote 439720 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:58:05] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:58:05] Using BAM RG (Read Group) ID: Resistance_28_fasta
[05:58:05] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:58:05] Running: bwa index reference/ref.fa 2>> snps.log
[05:58:11] Error running command, check Resistance_28_fasta/snps.log |
| 2 | [05:58:13] This is snippy 4.6.0Show full stderr[05:58:13] This is snippy 4.6.0
[05:58:13] Written by Torsten Seemann
[05:58:13] Obtained from https://github.com/tseemann/snippy
[05:58:13] Detected operating system: linux
[05:58:13] Enabling bundled linux tools.
[05:58:13] Found bwa - /usr/local/bin/bwa
[05:58:13] Found bcftools - /usr/local/bin/bcftools
[05:58:13] Found samtools - /usr/local/bin/samtools
[05:58:13] Found java - /usr/local/bin/java
[05:58:13] Found snpEff - /usr/local/bin/snpEff
[05:58:13] Found samclip - /usr/local/bin/samclip
[05:58:13] Found seqtk - /usr/local/bin/seqtk
[05:58:13] Found parallel - /usr/local/bin/parallel
[05:58:13] Found freebayes - /usr/local/bin/freebayes
[05:58:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:58:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:58:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:58:13] Found vcfuniq - /usr/local/bin/vcfuniq
[05:58:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:58:13] Found gzip - /bin/gzip
[05:58:13] Found vt - /usr/local/bin/vt
[05:58:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:58:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:58:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:58:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:58:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:58:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:58:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:58:14] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:58:14] Treating reference as 'fasta' format.
[05:58:14] Will use 1 CPU cores.
[05:58:14] Using read file: /corral4/main/objects/7/3/5/dataset_735d5f4d-4c45-4594-b696-4f2376c449f0.dat
[05:58:14] Creating folder: Resistance_63_fasta
[05:58:14] Changing working directory: Resistance_63_fasta
[05:58:14] Creating reference folder: reference
[05:58:14] Extracting FASTA and GFF from reference.
[05:58:15] Wrote 3 sequences to ref.fa
[05:58:15] Wrote 0 features to ref.gff
[05:58:15] Shredding /corral4/main/objects/7/3/5/dataset_735d5f4d-4c45-4594-b696-4f2376c449f0.dat into pseudo-reads
[05:58:19] Wrote 388254 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:58:19] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[05:58:19] Using BAM RG (Read Group) ID: Resistance_63_fasta
[05:58:19] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:58:19] Error running command, check Resistance_63_fasta/snps.log |
| 2 | [05:58:14] This is snippy 4.6.0Show full stderr[05:58:14] This is snippy 4.6.0
[05:58:14] Written by Torsten Seemann
[05:58:14] Obtained from https://github.com/tseemann/snippy
[05:58:14] Detected operating system: linux
[05:58:14] Enabling bundled linux tools.
[05:58:14] Found bwa - /usr/local/bin/bwa
[05:58:14] Found bcftools - /usr/local/bin/bcftools
[05:58:14] Found samtools - /usr/local/bin/samtools
[05:58:14] Found java - /usr/local/bin/java
[05:58:14] Found snpEff - /usr/local/bin/snpEff
[05:58:14] Found samclip - /usr/local/bin/samclip
[05:58:14] Found seqtk - /usr/local/bin/seqtk
[05:58:14] Found parallel - /usr/local/bin/parallel
[05:58:14] Found freebayes - /usr/local/bin/freebayes
[05:58:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:58:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:58:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:58:14] Found vcfuniq - /usr/local/bin/vcfuniq
[05:58:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:58:14] Found gzip - /bin/gzip
[05:58:14] Found vt - /usr/local/bin/vt
[05:58:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:58:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:58:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:58:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:58:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:58:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:58:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:58:16] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:58:16] Treating reference as 'fasta' format.
[05:58:16] Will use 1 CPU cores.
[05:58:16] Using read file: /corral4/main/objects/e/4/e/dataset_e4ec5ef2-d531-4a2f-bf23-97ecb3a510b7.dat
[05:58:16] Creating folder: Resistance_64_fasta
[05:58:16] Changing working directory: Resistance_64_fasta
[05:58:16] Creating reference folder: reference
[05:58:16] Extracting FASTA and GFF from reference.
[05:58:16] Wrote 3 sequences to ref.fa
[05:58:16] Wrote 0 features to ref.gff
[05:58:16] Shredding /corral4/main/objects/e/4/e/dataset_e4ec5ef2-d531-4a2f-bf23-97ecb3a510b7.dat into pseudo-reads
[05:58:20] Wrote 392922 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:58:20] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:58:20] Using BAM RG (Read Group) ID: Resistance_64_fasta
[05:58:20] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:58:20] Error running command, check Resistance_64_fasta/snps.log |
| 2 | [05:59:34] This is snippy 4.6.0Show full stderr[05:59:34] This is snippy 4.6.0
[05:59:34] Written by Torsten Seemann
[05:59:34] Obtained from https://github.com/tseemann/snippy
[05:59:34] Detected operating system: linux
[05:59:34] Enabling bundled linux tools.
[05:59:34] Found bwa - /usr/local/bin/bwa
[05:59:34] Found bcftools - /usr/local/bin/bcftools
[05:59:34] Found samtools - /usr/local/bin/samtools
[05:59:34] Found java - /usr/local/bin/java
[05:59:34] Found snpEff - /usr/local/bin/snpEff
[05:59:34] Found samclip - /usr/local/bin/samclip
[05:59:34] Found seqtk - /usr/local/bin/seqtk
[05:59:34] Found parallel - /usr/local/bin/parallel
[05:59:34] Found freebayes - /usr/local/bin/freebayes
[05:59:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:59:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:59:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:59:34] Found vcfuniq - /usr/local/bin/vcfuniq
[05:59:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:59:34] Found gzip - /bin/gzip
[05:59:34] Found vt - /usr/local/bin/vt
[05:59:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:59:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:59:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:59:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:59:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:59:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:59:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:59:35] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:59:35] Treating reference as 'fasta' format.
[05:59:35] Will use 1 CPU cores.
[05:59:35] Using read file: /corral4/main/objects/d/b/3/dataset_db3cd7c8-47c4-4b64-baf8-c75df54fe65c.dat
[05:59:35] Creating folder: Resistance_76_fasta
[05:59:35] Changing working directory: Resistance_76_fasta
[05:59:35] Creating reference folder: reference
[05:59:35] Extracting FASTA and GFF from reference.
[05:59:35] Wrote 3 sequences to ref.fa
[05:59:35] Wrote 0 features to ref.gff
[05:59:35] Shredding /corral4/main/objects/d/b/3/dataset_db3cd7c8-47c4-4b64-baf8-c75df54fe65c.dat into pseudo-reads
[05:59:40] Wrote 432130 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:59:40] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[05:59:40] Using BAM RG (Read Group) ID: Resistance_76_fasta
[05:59:40] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:59:40] Error running command, check Resistance_76_fasta/snps.log |
| 2 | [05:59:14] This is snippy 4.6.0Show full stderr[05:59:14] This is snippy 4.6.0
[05:59:14] Written by Torsten Seemann
[05:59:14] Obtained from https://github.com/tseemann/snippy
[05:59:14] Detected operating system: linux
[05:59:14] Enabling bundled linux tools.
[05:59:14] Found bwa - /usr/local/bin/bwa
[05:59:14] Found bcftools - /usr/local/bin/bcftools
[05:59:14] Found samtools - /usr/local/bin/samtools
[05:59:14] Found java - /usr/local/bin/java
[05:59:14] Found snpEff - /usr/local/bin/snpEff
[05:59:14] Found samclip - /usr/local/bin/samclip
[05:59:14] Found seqtk - /usr/local/bin/seqtk
[05:59:14] Found parallel - /usr/local/bin/parallel
[05:59:14] Found freebayes - /usr/local/bin/freebayes
[05:59:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:59:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:59:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:59:14] Found vcfuniq - /usr/local/bin/vcfuniq
[05:59:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:59:14] Found gzip - /bin/gzip
[05:59:14] Found vt - /usr/local/bin/vt
[05:59:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:59:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:59:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:59:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:59:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:59:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:59:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:59:16] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:59:16] Treating reference as 'fasta' format.
[05:59:16] Will use 1 CPU cores.
[05:59:16] Using read file: /corral4/main/objects/f/6/7/dataset_f670061e-7fa9-400e-85f8-fee756398e62.dat
[05:59:16] Creating folder: GCF_001191715_1_5505_8_8_genomic_fna
[05:59:16] Changing working directory: GCF_001191715_1_5505_8_8_genomic_fna
[05:59:16] Creating reference folder: reference
[05:59:16] Extracting FASTA and GFF from reference.
[05:59:16] Wrote 1 sequences to ref.fa
[05:59:16] Wrote 0 features to ref.gff
[05:59:16] Shredding /corral4/main/objects/f/6/7/dataset_f670061e-7fa9-400e-85f8-fee756398e62.dat into pseudo-reads
[05:59:20] Wrote 351090 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:59:21] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[05:59:21] Using BAM RG (Read Group) ID: GCF_001191715_1_5505_8_8_genomic_fna
[05:59:21] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:59:22] Error running command, check GCF_001191715_1_5505_8_8_genomic_fna/snps.log |
| 2 | [05:59:58] This is snippy 4.6.0Show full stderr[05:59:58] This is snippy 4.6.0
[05:59:58] Written by Torsten Seemann
[05:59:58] Obtained from https://github.com/tseemann/snippy
[05:59:58] Detected operating system: linux
[05:59:58] Enabling bundled linux tools.
[05:59:58] Found bwa - /usr/local/bin/bwa
[05:59:58] Found bcftools - /usr/local/bin/bcftools
[05:59:58] Found samtools - /usr/local/bin/samtools
[05:59:58] Found java - /usr/local/bin/java
[05:59:58] Found snpEff - /usr/local/bin/snpEff
[05:59:58] Found samclip - /usr/local/bin/samclip
[05:59:58] Found seqtk - /usr/local/bin/seqtk
[05:59:58] Found parallel - /usr/local/bin/parallel
[05:59:58] Found freebayes - /usr/local/bin/freebayes
[05:59:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:59:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:59:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:59:58] Found vcfuniq - /usr/local/bin/vcfuniq
[05:59:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:59:58] Found gzip - /bin/gzip
[05:59:58] Found vt - /usr/local/bin/vt
[05:59:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:59:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:59:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:59:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:59:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:59:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:59:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:59:59] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:59:59] Treating reference as 'fasta' format.
[05:59:59] Will use 1 CPU cores.
[05:59:59] Using read file: /corral4/main/objects/a/a/a/dataset_aaa5152b-fa66-4f0a-afc0-240761d2e97c.dat
[05:59:59] Creating folder: GCF_903992715_1_Q1142_genomic_fna
[05:59:59] Changing working directory: GCF_903992715_1_Q1142_genomic_fna
[05:59:59] Creating reference folder: reference
[05:59:59] Extracting FASTA and GFF from reference.
[06:00:00] Wrote 1 sequences to ref.fa
[06:00:00] Wrote 0 features to ref.gff
[06:00:00] Shredding /corral4/main/objects/a/a/a/dataset_aaa5152b-fa66-4f0a-afc0-240761d2e97c.dat into pseudo-reads
[06:00:03] Wrote 352422 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[06:00:04] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[06:00:04] Using BAM RG (Read Group) ID: GCF_903992715_1_Q1142_genomic_fna
[06:00:04] Running: samtools faidx reference/ref.fa 2>> snps.log
[06:00:04] Error running command, check GCF_903992715_1_Q1142_genomic_fna/snps.log |
| 2 | [06:00:07] This is snippy 4.6.0Show full stderr[06:00:07] This is snippy 4.6.0
[06:00:07] Written by Torsten Seemann
[06:00:07] Obtained from https://github.com/tseemann/snippy
[06:00:07] Detected operating system: linux
[06:00:07] Enabling bundled linux tools.
[06:00:07] Found bwa - /usr/local/bin/bwa
[06:00:07] Found bcftools - /usr/local/bin/bcftools
[06:00:07] Found samtools - /usr/local/bin/samtools
[06:00:07] Found java - /usr/local/bin/java
[06:00:07] Found snpEff - /usr/local/bin/snpEff
[06:00:07] Found samclip - /usr/local/bin/samclip
[06:00:07] Found seqtk - /usr/local/bin/seqtk
[06:00:07] Found parallel - /usr/local/bin/parallel
[06:00:07] Found freebayes - /usr/local/bin/freebayes
[06:00:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:00:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:00:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:00:07] Found vcfuniq - /usr/local/bin/vcfuniq
[06:00:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:00:07] Found gzip - /bin/gzip
[06:00:07] Found vt - /usr/local/bin/vt
[06:00:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:00:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:00:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:00:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:00:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:00:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:00:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:00:08] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[06:00:08] Treating reference as 'fasta' format.
[06:00:08] Will use 1 CPU cores.
[06:00:08] Using read file: /corral4/main/objects/2/5/d/dataset_25d0c2c3-35fe-47ff-a0ea-cd467baf8001.dat
[06:00:08] Creating folder: GCF_020536615_1_ASM2053661v1_genomic_fna
[06:00:08] Changing working directory: GCF_020536615_1_ASM2053661v1_genomic_fna
[06:00:08] Creating reference folder: reference
[06:00:08] Extracting FASTA and GFF from reference.
[06:00:08] Wrote 1 sequences to ref.fa
[06:00:08] Wrote 0 features to ref.gff
[06:00:08] Shredding /corral4/main/objects/2/5/d/dataset_25d0c2c3-35fe-47ff-a0ea-cd467baf8001.dat into pseudo-reads
[06:00:12] Wrote 349012 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[06:00:12] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time.
[06:00:12] Using BAM RG (Read Group) ID: GCF_020536615_1_ASM2053661v1_genomic_fna
[06:00:12] Running: samtools faidx reference/ref.fa 2>> snps.log
[06:00:12] Running: bwa index reference/ref.fa 2>> snps.log
[06:00:14] Error running command, check GCF_020536615_1_ASM2053661v1_genomic_fna/snps.log |
| 2 | [06:00:20] This is snippy 4.6.0Show full stderr[06:00:20] This is snippy 4.6.0
[06:00:20] Written by Torsten Seemann
[06:00:20] Obtained from https://github.com/tseemann/snippy
[06:00:20] Detected operating system: linux
[06:00:20] Enabling bundled linux tools.
[06:00:20] Found bwa - /usr/local/bin/bwa
[06:00:20] Found bcftools - /usr/local/bin/bcftools
[06:00:20] Found samtools - /usr/local/bin/samtools
[06:00:20] Found java - /usr/local/bin/java
[06:00:20] Found snpEff - /usr/local/bin/snpEff
[06:00:20] Found samclip - /usr/local/bin/samclip
[06:00:20] Found seqtk - /usr/local/bin/seqtk
[06:00:20] Found parallel - /usr/local/bin/parallel
[06:00:20] Found freebayes - /usr/local/bin/freebayes
[06:00:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:00:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:00:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:00:20] Found vcfuniq - /usr/local/bin/vcfuniq
[06:00:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:00:20] Found gzip - /bin/gzip
[06:00:20] Found vt - /usr/local/bin/vt
[06:00:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:00:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:00:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:00:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:00:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:00:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:00:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:00:21] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[06:00:21] Treating reference as 'fasta' format.
[06:00:21] Will use 1 CPU cores.
[06:00:21] Using read file: /corral4/main/objects/8/6/b/dataset_86be6f76-47ba-48f2-a1e3-44d60b33078a.dat
[06:00:21] Creating folder: GCF_902509475_1_Q0209_genomic_fna
[06:00:21] Changing working directory: GCF_902509475_1_Q0209_genomic_fna
[06:00:21] Creating reference folder: reference
[06:00:21] Extracting FASTA and GFF from reference.
[06:00:21] Wrote 1 sequences to ref.fa
[06:00:21] Wrote 0 features to ref.gff
[06:00:21] Shredding /corral4/main/objects/8/6/b/dataset_86be6f76-47ba-48f2-a1e3-44d60b33078a.dat into pseudo-reads
[06:00:24] Wrote 347750 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[06:00:24] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[06:00:24] Using BAM RG (Read Group) ID: GCF_902509475_1_Q0209_genomic_fna
[06:00:24] Running: samtools faidx reference/ref.fa 2>> snps.log
[06:00:24] Error running command, check GCF_902509475_1_Q0209_genomic_fna/snps.log |
| 2 | [06:58:21] This is snippy 4.6.0Show full stderr[06:58:21] This is snippy 4.6.0
[06:58:21] Written by Torsten Seemann
[06:58:21] Obtained from https://github.com/tseemann/snippy
[06:58:21] Detected operating system: linux
[06:58:21] Enabling bundled linux tools.
[06:58:21] Found bwa - /usr/local/bin/bwa
[06:58:21] Found bcftools - /usr/local/bin/bcftools
[06:58:21] Found samtools - /usr/local/bin/samtools
[06:58:21] Found java - /usr/local/bin/java
[06:58:21] Found snpEff - /usr/local/bin/snpEff
[06:58:21] Found samclip - /usr/local/bin/samclip
[06:58:21] Found seqtk - /usr/local/bin/seqtk
[06:58:21] Found parallel - /usr/local/bin/parallel
[06:58:21] Found freebayes - /usr/local/bin/freebayes
[06:58:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:21] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:21] Found gzip - /bin/gzip
[06:58:21] Found vt - /usr/local/bin/vt
[06:58:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:22] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[06:58:22] Treating reference as 'fasta' format.
[06:58:22] Will use 1 CPU cores.
[06:58:22] Using read file: /corral4/main/objects/0/e/9/dataset_0e967aab-1d11-4057-ab74-1b27a9a4c8ef.dat
[06:58:22] Creating folder: BVBRC_genome_sequence__78__fasta
[06:58:22] Changing working directory: BVBRC_genome_sequence__78__fasta
[06:58:22] Creating reference folder: reference
[06:58:22] Extracting FASTA and GFF from reference.
[06:58:22] Wrote 1 sequences to ref.fa
[06:58:22] Wrote 0 features to ref.gff
[06:58:22] Shredding /corral4/main/objects/0/e/9/dataset_0e967aab-1d11-4057-ab74-1b27a9a4c8ef.dat into pseudo-reads
[06:58:24] Wrote 216932 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[06:58:24] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[06:58:24] Using BAM RG (Read Group) ID: BVBRC_genome_sequence__78__fasta
[06:58:24] Running: samtools faidx reference/ref.fa 2>> snps.log
[06:58:24] Running: bwa index reference/ref.fa 2>> snps.log
[06:58:26] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[06:58:26] Running: ln -sf reference/ref.fa . 2>> snps.log
[06:58:26] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[06:58:26] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[06:58:26] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence__78__fasta\tSM:BVBRC_genome_sequence__78__fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261283/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261283/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261283/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[s |
| 2 | [07:02:34] This is snippy 4.6.0Show full stderr[07:02:34] This is snippy 4.6.0
[07:02:34] Written by Torsten Seemann
[07:02:34] Obtained from https://github.com/tseemann/snippy
[07:02:34] Detected operating system: linux
[07:02:34] Enabling bundled linux tools.
[07:02:34] Found bwa - /usr/local/bin/bwa
[07:02:34] Found bcftools - /usr/local/bin/bcftools
[07:02:34] Found samtools - /usr/local/bin/samtools
[07:02:34] Found java - /usr/local/bin/java
[07:02:34] Found snpEff - /usr/local/bin/snpEff
[07:02:34] Found samclip - /usr/local/bin/samclip
[07:02:34] Found seqtk - /usr/local/bin/seqtk
[07:02:34] Found parallel - /usr/local/bin/parallel
[07:02:34] Found freebayes - /usr/local/bin/freebayes
[07:02:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:02:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:02:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:02:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:02:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:02:34] Found gzip - /bin/gzip
[07:02:34] Found vt - /usr/local/bin/vt
[07:02:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:02:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:02:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:02:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:02:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:02:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:02:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:02:35] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:02:35] Treating reference as 'fasta' format.
[07:02:35] Will use 1 CPU cores.
[07:02:35] Using read file: /corral4/main/objects/5/9/5/dataset_5955a17d-5755-4d34-b4d0-d5f37647b470.dat
[07:02:35] Creating folder: BVBRC_genome_sequence___2025_10_25T135642_512_fasta
[07:02:35] Changing working directory: BVBRC_genome_sequence___2025_10_25T135642_512_fasta
[07:02:35] Creating reference folder: reference
[07:02:35] Extracting FASTA and GFF from reference.
[07:02:35] Wrote 1 sequences to ref.fa
[07:02:35] Wrote 0 features to ref.gff
[07:02:35] Shredding /corral4/main/objects/5/9/5/dataset_5955a17d-5755-4d34-b4d0-d5f37647b470.dat into pseudo-reads
[07:02:37] Wrote 222668 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:02:37] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[07:02:37] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135642_512_fasta
[07:02:37] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:02:37] Running: bwa index reference/ref.fa 2>> snps.log
[07:02:38] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[07:02:38] Running: ln -sf reference/ref.fa . 2>> snps.log
[07:02:38] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[07:02:38] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[07:02:38] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135642_512_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135642_512_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261358/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261358/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261358/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samcl |
| 2 | [07:05:38] This is snippy 4.6.0Show full stderr[07:05:38] This is snippy 4.6.0
[07:05:38] Written by Torsten Seemann
[07:05:38] Obtained from https://github.com/tseemann/snippy
[07:05:38] Detected operating system: linux
[07:05:38] Enabling bundled linux tools.
[07:05:38] Found bwa - /usr/local/bin/bwa
[07:05:38] Found bcftools - /usr/local/bin/bcftools
[07:05:38] Found samtools - /usr/local/bin/samtools
[07:05:38] Found java - /usr/local/bin/java
[07:05:38] Found snpEff - /usr/local/bin/snpEff
[07:05:38] Found samclip - /usr/local/bin/samclip
[07:05:38] Found seqtk - /usr/local/bin/seqtk
[07:05:38] Found parallel - /usr/local/bin/parallel
[07:05:38] Found freebayes - /usr/local/bin/freebayes
[07:05:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:38] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:38] Found gzip - /bin/gzip
[07:05:38] Found vt - /usr/local/bin/vt
[07:05:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:39] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:05:39] Treating reference as 'fasta' format.
[07:05:39] Will use 1 CPU cores.
[07:05:39] Using read file: /corral4/main/objects/3/2/7/dataset_3270deb9-a273-4d32-9777-15dcab5bd02b.dat
[07:05:39] Creating folder: BVBRC_genome_sequence___2025_10_25T135710_500_fasta
[07:05:39] Changing working directory: BVBRC_genome_sequence___2025_10_25T135710_500_fasta
[07:05:39] Creating reference folder: reference
[07:05:39] Extracting FASTA and GFF from reference.
[07:05:39] Wrote 1 sequences to ref.fa
[07:05:39] Wrote 0 features to ref.gff
[07:05:39] Shredding /corral4/main/objects/3/2/7/dataset_3270deb9-a273-4d32-9777-15dcab5bd02b.dat into pseudo-reads
[07:05:41] Wrote 222136 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:05:41] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[07:05:41] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135710_500_fasta
[07:05:41] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:05:41] Error running command, check BVBRC_genome_sequence___2025_10_25T135710_500_fasta/snps.log |
| 2 | [07:05:54] This is snippy 4.6.0Show full stderr[07:05:54] This is snippy 4.6.0
[07:05:54] Written by Torsten Seemann
[07:05:54] Obtained from https://github.com/tseemann/snippy
[07:05:54] Detected operating system: linux
[07:05:54] Enabling bundled linux tools.
[07:05:54] Found bwa - /usr/local/bin/bwa
[07:05:54] Found bcftools - /usr/local/bin/bcftools
[07:05:54] Found samtools - /usr/local/bin/samtools
[07:05:54] Found java - /usr/local/bin/java
[07:05:54] Found snpEff - /usr/local/bin/snpEff
[07:05:54] Found samclip - /usr/local/bin/samclip
[07:05:54] Found seqtk - /usr/local/bin/seqtk
[07:05:54] Found parallel - /usr/local/bin/parallel
[07:05:54] Found freebayes - /usr/local/bin/freebayes
[07:05:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:54] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:54] Found gzip - /bin/gzip
[07:05:54] Found vt - /usr/local/bin/vt
[07:05:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:55] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:05:55] Treating reference as 'fasta' format.
[07:05:55] Will use 1 CPU cores.
[07:05:55] Using read file: /corral4/main/objects/5/a/2/dataset_5a2a9927-9c17-4e2c-9090-63a02a9141b0.dat
[07:05:55] Creating folder: BVBRC_genome_sequence___2025_10_25T135715_719_fasta
[07:05:55] Changing working directory: BVBRC_genome_sequence___2025_10_25T135715_719_fasta
[07:05:55] Creating reference folder: reference
[07:05:55] Extracting FASTA and GFF from reference.
[07:05:55] Wrote 1 sequences to ref.fa
[07:05:55] Wrote 0 features to ref.gff
[07:05:55] Shredding /corral4/main/objects/5/a/2/dataset_5a2a9927-9c17-4e2c-9090-63a02a9141b0.dat into pseudo-reads
[07:05:57] Wrote 224908 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:05:57] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[07:05:57] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135715_719_fasta
[07:05:57] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:05:57] Running: bwa index reference/ref.fa 2>> snps.log
[07:05:59] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[07:05:59] Running: ln -sf reference/ref.fa . 2>> snps.log
[07:05:59] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[07:05:59] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[07:05:59] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135715_719_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135715_719_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261365/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261365/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261365/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log |
| 2 | [06:47:56] This is snippy 4.6.0Show full stderr[06:47:56] This is snippy 4.6.0
[06:47:56] Written by Torsten Seemann
[06:47:56] Obtained from https://github.com/tseemann/snippy
[06:47:56] Detected operating system: linux
[06:47:56] Enabling bundled linux tools.
[06:47:56] Found bwa - /usr/local/bin/bwa
[06:47:56] Found bcftools - /usr/local/bin/bcftools
[06:47:56] Found samtools - /usr/local/bin/samtools
[06:47:56] Found java - /usr/local/bin/java
[06:47:56] Found snpEff - /usr/local/bin/snpEff
[06:47:56] Found samclip - /usr/local/bin/samclip
[06:47:56] Found seqtk - /usr/local/bin/seqtk
[06:47:56] Found parallel - /usr/local/bin/parallel
[06:47:56] Found freebayes - /usr/local/bin/freebayes
[06:47:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:47:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:47:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:47:56] Found vcfuniq - /usr/local/bin/vcfuniq
[06:47:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:47:56] Found gzip - /bin/gzip
[06:47:56] Found vt - /usr/local/bin/vt
[06:47:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:47:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:47:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:47:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:47:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:47:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:47:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:47:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:00:09] This is snippy 4.6.0Show full stderr[07:00:09] This is snippy 4.6.0
[07:00:09] Written by Torsten Seemann
[07:00:09] Obtained from https://github.com/tseemann/snippy
[07:00:09] Detected operating system: linux
[07:00:09] Enabling bundled linux tools.
[07:00:09] Found bwa - /usr/local/bin/bwa
[07:00:09] Found bcftools - /usr/local/bin/bcftools
[07:00:09] Found samtools - /usr/local/bin/samtools
[07:00:09] Found java - /usr/local/bin/java
[07:00:09] Found snpEff - /usr/local/bin/snpEff
[07:00:09] Found samclip - /usr/local/bin/samclip
[07:00:09] Found seqtk - /usr/local/bin/seqtk
[07:00:09] Found parallel - /usr/local/bin/parallel
[07:00:09] Found freebayes - /usr/local/bin/freebayes
[07:00:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:09] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:09] Found gzip - /bin/gzip
[07:00:09] Found vt - /usr/local/bin/vt
[07:00:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:49:07] This is snippy 4.6.0Show full stderr[06:49:07] This is snippy 4.6.0
[06:49:07] Written by Torsten Seemann
[06:49:07] Obtained from https://github.com/tseemann/snippy
[06:49:07] Detected operating system: linux
[06:49:07] Enabling bundled linux tools.
[06:49:07] Found bwa - /usr/local/bin/bwa
[06:49:07] Found bcftools - /usr/local/bin/bcftools
[06:49:07] Found samtools - /usr/local/bin/samtools
[06:49:07] Found java - /usr/local/bin/java
[06:49:07] Found snpEff - /usr/local/bin/snpEff
[06:49:07] Found samclip - /usr/local/bin/samclip
[06:49:07] Found seqtk - /usr/local/bin/seqtk
[06:49:07] Found parallel - /usr/local/bin/parallel
[06:49:07] Found freebayes - /usr/local/bin/freebayes
[06:49:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:49:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:49:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:49:07] Found vcfuniq - /usr/local/bin/vcfuniq
[06:49:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:49:07] Found gzip - /bin/gzip
[06:49:07] Found vt - /usr/local/bin/vt
[06:49:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:49:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:49:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:49:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:49:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:49:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:49:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:49:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:49:10] This is snippy 4.6.0Show full stderr[06:49:10] This is snippy 4.6.0
[06:49:10] Written by Torsten Seemann
[06:49:10] Obtained from https://github.com/tseemann/snippy
[06:49:10] Detected operating system: linux
[06:49:10] Enabling bundled linux tools.
[06:49:10] Found bwa - /usr/local/bin/bwa
[06:49:10] Found bcftools - /usr/local/bin/bcftools
[06:49:10] Found samtools - /usr/local/bin/samtools
[06:49:10] Found java - /usr/local/bin/java
[06:49:10] Found snpEff - /usr/local/bin/snpEff
[06:49:10] Found samclip - /usr/local/bin/samclip
[06:49:10] Found seqtk - /usr/local/bin/seqtk
[06:49:10] Found parallel - /usr/local/bin/parallel
[06:49:10] Found freebayes - /usr/local/bin/freebayes
[06:49:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:49:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:49:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:49:10] Found vcfuniq - /usr/local/bin/vcfuniq
[06:49:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:49:10] Found gzip - /bin/gzip
[06:49:10] Found vt - /usr/local/bin/vt
[06:49:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:49:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:49:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:49:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:49:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:49:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:49:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:49:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:49:22] This is snippy 4.6.0Show full stderr[06:49:22] This is snippy 4.6.0
[06:49:22] Written by Torsten Seemann
[06:49:22] Obtained from https://github.com/tseemann/snippy
[06:49:22] Detected operating system: linux
[06:49:22] Enabling bundled linux tools.
[06:49:22] Found bwa - /usr/local/bin/bwa
[06:49:22] Found bcftools - /usr/local/bin/bcftools
[06:49:22] Found samtools - /usr/local/bin/samtools
[06:49:22] Found java - /usr/local/bin/java
[06:49:22] Found snpEff - /usr/local/bin/snpEff
[06:49:22] Found samclip - /usr/local/bin/samclip
[06:49:22] Found seqtk - /usr/local/bin/seqtk
[06:49:22] Found parallel - /usr/local/bin/parallel
[06:49:22] Found freebayes - /usr/local/bin/freebayes
[06:49:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:49:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:49:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:49:22] Found vcfuniq - /usr/local/bin/vcfuniq
[06:49:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:49:22] Found gzip - /bin/gzip
[06:49:22] Found vt - /usr/local/bin/vt
[06:49:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:49:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:49:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:49:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:49:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:49:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:49:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:49:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:53:48] This is snippy 4.6.0Show full stderr[06:53:48] This is snippy 4.6.0
[06:53:48] Written by Torsten Seemann
[06:53:48] Obtained from https://github.com/tseemann/snippy
[06:53:48] Detected operating system: linux
[06:53:48] Enabling bundled linux tools.
[06:53:48] Found bwa - /usr/local/bin/bwa
[06:53:48] Found bcftools - /usr/local/bin/bcftools
[06:53:48] Found samtools - /usr/local/bin/samtools
[06:53:48] Found java - /usr/local/bin/java
[06:53:48] Found snpEff - /usr/local/bin/snpEff
[06:53:48] Found samclip - /usr/local/bin/samclip
[06:53:48] Found seqtk - /usr/local/bin/seqtk
[06:53:48] Found parallel - /usr/local/bin/parallel
[06:53:48] Found freebayes - /usr/local/bin/freebayes
[06:53:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:48] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:48] Found gzip - /bin/gzip
[06:53:48] Found vt - /usr/local/bin/vt
[06:53:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:00:10] This is snippy 4.6.0Show full stderr[07:00:10] This is snippy 4.6.0
[07:00:10] Written by Torsten Seemann
[07:00:10] Obtained from https://github.com/tseemann/snippy
[07:00:10] Detected operating system: linux
[07:00:10] Enabling bundled linux tools.
[07:00:10] Found bwa - /usr/local/bin/bwa
[07:00:10] Found bcftools - /usr/local/bin/bcftools
[07:00:10] Found samtools - /usr/local/bin/samtools
[07:00:10] Found java - /usr/local/bin/java
[07:00:10] Found snpEff - /usr/local/bin/snpEff
[07:00:10] Found samclip - /usr/local/bin/samclip
[07:00:10] Found seqtk - /usr/local/bin/seqtk
[07:00:10] Found parallel - /usr/local/bin/parallel
[07:00:10] Found freebayes - /usr/local/bin/freebayes
[07:00:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:10] Found gzip - /bin/gzip
[07:00:10] Found vt - /usr/local/bin/vt
[07:00:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:07:28] This is snippy 4.6.0Show full stderr[07:07:28] This is snippy 4.6.0
[07:07:28] Written by Torsten Seemann
[07:07:28] Obtained from https://github.com/tseemann/snippy
[07:07:28] Detected operating system: linux
[07:07:28] Enabling bundled linux tools.
[07:07:28] Found bwa - /usr/local/bin/bwa
[07:07:28] Found bcftools - /usr/local/bin/bcftools
[07:07:28] Found samtools - /usr/local/bin/samtools
[07:07:28] Found java - /usr/local/bin/java
[07:07:28] Found snpEff - /usr/local/bin/snpEff
[07:07:28] Found samclip - /usr/local/bin/samclip
[07:07:28] Found seqtk - /usr/local/bin/seqtk
[07:07:28] Found parallel - /usr/local/bin/parallel
[07:07:28] Found freebayes - /usr/local/bin/freebayes
[07:07:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:28] Found gzip - /bin/gzip
[07:07:28] Found vt - /usr/local/bin/vt
[07:07:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:48:39] This is snippy 4.6.0Show full stderr[06:48:39] This is snippy 4.6.0
[06:48:39] Written by Torsten Seemann
[06:48:39] Obtained from https://github.com/tseemann/snippy
[06:48:39] Detected operating system: linux
[06:48:39] Enabling bundled linux tools.
[06:48:39] Found bwa - /usr/local/bin/bwa
[06:48:39] Found bcftools - /usr/local/bin/bcftools
[06:48:39] Found samtools - /usr/local/bin/samtools
[06:48:39] Found java - /usr/local/bin/java
[06:48:39] Found snpEff - /usr/local/bin/snpEff
[06:48:39] Found samclip - /usr/local/bin/samclip
[06:48:39] Found seqtk - /usr/local/bin/seqtk
[06:48:39] Found parallel - /usr/local/bin/parallel
[06:48:39] Found freebayes - /usr/local/bin/freebayes
[06:48:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:39] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:39] Found gzip - /bin/gzip
[06:48:39] Found vt - /usr/local/bin/vt
[06:48:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:49:36] This is snippy 4.6.0Show full stderr[06:49:36] This is snippy 4.6.0
[06:49:36] Written by Torsten Seemann
[06:49:36] Obtained from https://github.com/tseemann/snippy
[06:49:36] Detected operating system: linux
[06:49:36] Enabling bundled linux tools.
[06:49:36] Found bwa - /usr/local/bin/bwa
[06:49:36] Found bcftools - /usr/local/bin/bcftools
[06:49:36] Found samtools - /usr/local/bin/samtools
[06:49:36] Found java - /usr/local/bin/java
[06:49:36] Found snpEff - /usr/local/bin/snpEff
[06:49:36] Found samclip - /usr/local/bin/samclip
[06:49:36] Found seqtk - /usr/local/bin/seqtk
[06:49:36] Found parallel - /usr/local/bin/parallel
[06:49:36] Found freebayes - /usr/local/bin/freebayes
[06:49:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:49:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:49:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:49:36] Found vcfuniq - /usr/local/bin/vcfuniq
[06:49:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:49:36] Found gzip - /bin/gzip
[06:49:36] Found vt - /usr/local/bin/vt
[06:49:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:49:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:49:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:49:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:49:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:49:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:49:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:49:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:38:54] This is snippy 4.6.0Show full stderr[07:38:54] This is snippy 4.6.0
[07:38:54] Written by Torsten Seemann
[07:38:54] Obtained from https://github.com/tseemann/snippy
[07:38:54] Detected operating system: linux
[07:38:54] Enabling bundled linux tools.
[07:38:54] Found bwa - /usr/local/bin/bwa
[07:38:54] Found bcftools - /usr/local/bin/bcftools
[07:38:54] Found samtools - /usr/local/bin/samtools
[07:38:54] Found java - /usr/local/bin/java
[07:38:54] Found snpEff - /usr/local/bin/snpEff
[07:38:54] Found samclip - /usr/local/bin/samclip
[07:38:54] Found seqtk - /usr/local/bin/seqtk
[07:38:54] Found parallel - /usr/local/bin/parallel
[07:38:54] Found freebayes - /usr/local/bin/freebayes
[07:38:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:54] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:54] Found gzip - /bin/gzip
[07:38:54] Found vt - /usr/local/bin/vt
[07:38:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:45:13] This is snippy 4.6.0Show full stderr[07:45:13] This is snippy 4.6.0
[07:45:13] Written by Torsten Seemann
[07:45:13] Obtained from https://github.com/tseemann/snippy
[07:45:13] Detected operating system: linux
[07:45:13] Enabling bundled linux tools.
[07:45:13] Found bwa - /usr/local/bin/bwa
[07:45:13] Found bcftools - /usr/local/bin/bcftools
[07:45:13] Found samtools - /usr/local/bin/samtools
[07:45:13] Found java - /usr/local/bin/java
[07:45:13] Found snpEff - /usr/local/bin/snpEff
[07:45:13] Found samclip - /usr/local/bin/samclip
[07:45:13] Found seqtk - /usr/local/bin/seqtk
[07:45:13] Found parallel - /usr/local/bin/parallel
[07:45:13] Found freebayes - /usr/local/bin/freebayes
[07:45:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:13] Found gzip - /bin/gzip
[07:45:13] Found vt - /usr/local/bin/vt
[07:45:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:51:04] This is snippy 4.6.0Show full stderr[06:51:04] This is snippy 4.6.0
[06:51:04] Written by Torsten Seemann
[06:51:04] Obtained from https://github.com/tseemann/snippy
[06:51:04] Detected operating system: linux
[06:51:04] Enabling bundled linux tools.
[06:51:04] Found bwa - /usr/local/bin/bwa
[06:51:04] Found bcftools - /usr/local/bin/bcftools
[06:51:04] Found samtools - /usr/local/bin/samtools
[06:51:04] Found java - /usr/local/bin/java
[06:51:04] Found snpEff - /usr/local/bin/snpEff
[06:51:04] Found samclip - /usr/local/bin/samclip
[06:51:04] Found seqtk - /usr/local/bin/seqtk
[06:51:04] Found parallel - /usr/local/bin/parallel
[06:51:04] Found freebayes - /usr/local/bin/freebayes
[06:51:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:51:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:51:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:51:04] Found vcfuniq - /usr/local/bin/vcfuniq
[06:51:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:51:04] Found gzip - /bin/gzip
[06:51:04] Found vt - /usr/local/bin/vt
[06:51:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:51:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:51:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:51:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:51:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:51:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:51:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:51:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:51:15] This is snippy 4.6.0Show full stderr[07:51:15] This is snippy 4.6.0
[07:51:15] Written by Torsten Seemann
[07:51:15] Obtained from https://github.com/tseemann/snippy
[07:51:15] Detected operating system: linux
[07:51:15] Enabling bundled linux tools.
[07:51:15] Found bwa - /usr/local/bin/bwa
[07:51:15] Found bcftools - /usr/local/bin/bcftools
[07:51:15] Found samtools - /usr/local/bin/samtools
[07:51:15] Found java - /usr/local/bin/java
[07:51:15] Found snpEff - /usr/local/bin/snpEff
[07:51:15] Found samclip - /usr/local/bin/samclip
[07:51:15] Found seqtk - /usr/local/bin/seqtk
[07:51:15] Found parallel - /usr/local/bin/parallel
[07:51:15] Found freebayes - /usr/local/bin/freebayes
[07:51:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:51:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:51:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:51:15] Found vcfuniq - /usr/local/bin/vcfuniq
[07:51:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:51:15] Found gzip - /bin/gzip
[07:51:15] Found vt - /usr/local/bin/vt
[07:51:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:51:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:51:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:51:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:51:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:51:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:51:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:51:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:51:14] This is snippy 4.6.0Show full stderr[06:51:14] This is snippy 4.6.0
[06:51:14] Written by Torsten Seemann
[06:51:14] Obtained from https://github.com/tseemann/snippy
[06:51:14] Detected operating system: linux
[06:51:14] Enabling bundled linux tools.
[06:51:14] Found bwa - /usr/local/bin/bwa
[06:51:14] Found bcftools - /usr/local/bin/bcftools
[06:51:14] Found samtools - /usr/local/bin/samtools
[06:51:14] Found java - /usr/local/bin/java
[06:51:14] Found snpEff - /usr/local/bin/snpEff
[06:51:14] Found samclip - /usr/local/bin/samclip
[06:51:14] Found seqtk - /usr/local/bin/seqtk
[06:51:14] Found parallel - /usr/local/bin/parallel
[06:51:14] Found freebayes - /usr/local/bin/freebayes
[06:51:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:51:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:51:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:51:14] Found vcfuniq - /usr/local/bin/vcfuniq
[06:51:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:51:14] Found gzip - /bin/gzip
[06:51:14] Found vt - /usr/local/bin/vt
[06:51:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:51:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:51:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:51:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:51:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:51:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:51:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:51:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:52:36] This is snippy 4.6.0Show full stderr[06:52:36] This is snippy 4.6.0
[06:52:36] Written by Torsten Seemann
[06:52:36] Obtained from https://github.com/tseemann/snippy
[06:52:36] Detected operating system: linux
[06:52:36] Enabling bundled linux tools.
[06:52:36] Found bwa - /usr/local/bin/bwa
[06:52:36] Found bcftools - /usr/local/bin/bcftools
[06:52:36] Found samtools - /usr/local/bin/samtools
[06:52:36] Found java - /usr/local/bin/java
[06:52:36] Found snpEff - /usr/local/bin/snpEff
[06:52:36] Found samclip - /usr/local/bin/samclip
[06:52:36] Found seqtk - /usr/local/bin/seqtk
[06:52:36] Found parallel - /usr/local/bin/parallel
[06:52:36] Found freebayes - /usr/local/bin/freebayes
[06:52:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:36] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:36] Found gzip - /bin/gzip
[06:52:36] Found vt - /usr/local/bin/vt
[06:52:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:53:18] This is snippy 4.6.0Show full stderr[06:53:18] This is snippy 4.6.0
[06:53:18] Written by Torsten Seemann
[06:53:18] Obtained from https://github.com/tseemann/snippy
[06:53:18] Detected operating system: linux
[06:53:18] Enabling bundled linux tools.
[06:53:18] Found bwa - /usr/local/bin/bwa
[06:53:18] Found bcftools - /usr/local/bin/bcftools
[06:53:18] Found samtools - /usr/local/bin/samtools
[06:53:18] Found java - /usr/local/bin/java
[06:53:18] Found snpEff - /usr/local/bin/snpEff
[06:53:18] Found samclip - /usr/local/bin/samclip
[06:53:18] Found seqtk - /usr/local/bin/seqtk
[06:53:18] Found parallel - /usr/local/bin/parallel
[06:53:18] Found freebayes - /usr/local/bin/freebayes
[06:53:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:18] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:18] Found gzip - /bin/gzip
[06:53:18] Found vt - /usr/local/bin/vt
[06:53:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:53:30] This is snippy 4.6.0Show full stderr[06:53:30] This is snippy 4.6.0
[06:53:30] Written by Torsten Seemann
[06:53:30] Obtained from https://github.com/tseemann/snippy
[06:53:30] Detected operating system: linux
[06:53:30] Enabling bundled linux tools.
[06:53:30] Found bwa - /usr/local/bin/bwa
[06:53:30] Found bcftools - /usr/local/bin/bcftools
[06:53:30] Found samtools - /usr/local/bin/samtools
[06:53:30] Found java - /usr/local/bin/java
[06:53:30] Found snpEff - /usr/local/bin/snpEff
[06:53:30] Found samclip - /usr/local/bin/samclip
[06:53:30] Found seqtk - /usr/local/bin/seqtk
[06:53:30] Found parallel - /usr/local/bin/parallel
[06:53:30] Found freebayes - /usr/local/bin/freebayes
[06:53:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:30] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:30] Found gzip - /bin/gzip
[06:53:30] Found vt - /usr/local/bin/vt
[06:53:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:50:53] This is snippy 4.6.0Show full stderr[06:50:53] This is snippy 4.6.0
[06:50:53] Written by Torsten Seemann
[06:50:53] Obtained from https://github.com/tseemann/snippy
[06:50:53] Detected operating system: linux
[06:50:53] Enabling bundled linux tools.
[06:50:53] Found bwa - /usr/local/bin/bwa
[06:50:53] Found bcftools - /usr/local/bin/bcftools
[06:50:53] Found samtools - /usr/local/bin/samtools
[06:50:53] Found java - /usr/local/bin/java
[06:50:53] Found snpEff - /usr/local/bin/snpEff
[06:50:53] Found samclip - /usr/local/bin/samclip
[06:50:53] Found seqtk - /usr/local/bin/seqtk
[06:50:53] Found parallel - /usr/local/bin/parallel
[06:50:53] Found freebayes - /usr/local/bin/freebayes
[06:50:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:50:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:50:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:50:53] Found vcfuniq - /usr/local/bin/vcfuniq
[06:50:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:50:53] Found gzip - /bin/gzip
[06:50:53] Found vt - /usr/local/bin/vt
[06:50:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:50:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:50:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:50:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:50:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:50:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:50:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:50:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [08:03:31] This is snippy 4.6.0Show full stderr[08:03:31] This is snippy 4.6.0
[08:03:31] Written by Torsten Seemann
[08:03:31] Obtained from https://github.com/tseemann/snippy
[08:03:31] Detected operating system: linux
[08:03:31] Enabling bundled linux tools.
[08:03:31] Found bwa - /usr/local/bin/bwa
[08:03:31] Found bcftools - /usr/local/bin/bcftools
[08:03:31] Found samtools - /usr/local/bin/samtools
[08:03:31] Found java - /usr/local/bin/java
[08:03:31] Found snpEff - /usr/local/bin/snpEff
[08:03:31] Found samclip - /usr/local/bin/samclip
[08:03:31] Found seqtk - /usr/local/bin/seqtk
[08:03:31] Found parallel - /usr/local/bin/parallel
[08:03:31] Found freebayes - /usr/local/bin/freebayes
[08:03:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:03:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:03:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:03:31] Found vcfuniq - /usr/local/bin/vcfuniq
[08:03:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:03:31] Found gzip - /bin/gzip
[08:03:31] Found vt - /usr/local/bin/vt
[08:03:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:03:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:03:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:03:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:03:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:03:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:03:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:03:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:53:36] This is snippy 4.6.0Show full stderr[06:53:36] This is snippy 4.6.0
[06:53:36] Written by Torsten Seemann
[06:53:36] Obtained from https://github.com/tseemann/snippy
[06:53:36] Detected operating system: linux
[06:53:36] Enabling bundled linux tools.
[06:53:36] Found bwa - /usr/local/bin/bwa
[06:53:36] Found bcftools - /usr/local/bin/bcftools
[06:53:36] Found samtools - /usr/local/bin/samtools
[06:53:36] Found java - /usr/local/bin/java
[06:53:36] Found snpEff - /usr/local/bin/snpEff
[06:53:36] Found samclip - /usr/local/bin/samclip
[06:53:36] Found seqtk - /usr/local/bin/seqtk
[06:53:36] Found parallel - /usr/local/bin/parallel
[06:53:36] Found freebayes - /usr/local/bin/freebayes
[06:53:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:36] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:36] Found gzip - /bin/gzip
[06:53:36] Found vt - /usr/local/bin/vt
[06:53:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:53:44] This is snippy 4.6.0Show full stderr[06:53:44] This is snippy 4.6.0
[06:53:44] Written by Torsten Seemann
[06:53:44] Obtained from https://github.com/tseemann/snippy
[06:53:44] Detected operating system: linux
[06:53:44] Enabling bundled linux tools.
[06:53:44] Found bwa - /usr/local/bin/bwa
[06:53:44] Found bcftools - /usr/local/bin/bcftools
[06:53:44] Found samtools - /usr/local/bin/samtools
[06:53:44] Found java - /usr/local/bin/java
[06:53:44] Found snpEff - /usr/local/bin/snpEff
[06:53:44] Found samclip - /usr/local/bin/samclip
[06:53:44] Found seqtk - /usr/local/bin/seqtk
[06:53:44] Found parallel - /usr/local/bin/parallel
[06:53:44] Found freebayes - /usr/local/bin/freebayes
[06:53:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:44] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:44] Found gzip - /bin/gzip
[06:53:44] Found vt - /usr/local/bin/vt
[06:53:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:54:14] This is snippy 4.6.0Show full stderr[06:54:14] This is snippy 4.6.0
[06:54:14] Written by Torsten Seemann
[06:54:14] Obtained from https://github.com/tseemann/snippy
[06:54:14] Detected operating system: linux
[06:54:14] Enabling bundled linux tools.
[06:54:14] Found bwa - /usr/local/bin/bwa
[06:54:14] Found bcftools - /usr/local/bin/bcftools
[06:54:14] Found samtools - /usr/local/bin/samtools
[06:54:14] Found java - /usr/local/bin/java
[06:54:14] Found snpEff - /usr/local/bin/snpEff
[06:54:14] Found samclip - /usr/local/bin/samclip
[06:54:14] Found seqtk - /usr/local/bin/seqtk
[06:54:14] Found parallel - /usr/local/bin/parallel
[06:54:14] Found freebayes - /usr/local/bin/freebayes
[06:54:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:14] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:14] Found gzip - /bin/gzip
[06:54:14] Found vt - /usr/local/bin/vt
[06:54:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:52:22] This is snippy 4.6.0Show full stderr[06:52:22] This is snippy 4.6.0
[06:52:22] Written by Torsten Seemann
[06:52:22] Obtained from https://github.com/tseemann/snippy
[06:52:22] Detected operating system: linux
[06:52:22] Enabling bundled linux tools.
[06:52:22] Found bwa - /usr/local/bin/bwa
[06:52:22] Found bcftools - /usr/local/bin/bcftools
[06:52:22] Found samtools - /usr/local/bin/samtools
[06:52:22] Found java - /usr/local/bin/java
[06:52:22] Found snpEff - /usr/local/bin/snpEff
[06:52:22] Found samclip - /usr/local/bin/samclip
[06:52:22] Found seqtk - /usr/local/bin/seqtk
[06:52:22] Found parallel - /usr/local/bin/parallel
[06:52:22] Found freebayes - /usr/local/bin/freebayes
[06:52:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:22] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:22] Found gzip - /bin/gzip
[06:52:22] Found vt - /usr/local/bin/vt
[06:52:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:52:51] This is snippy 4.6.0Show full stderr[06:52:51] This is snippy 4.6.0
[06:52:51] Written by Torsten Seemann
[06:52:51] Obtained from https://github.com/tseemann/snippy
[06:52:51] Detected operating system: linux
[06:52:51] Enabling bundled linux tools.
[06:52:51] Found bwa - /usr/local/bin/bwa
[06:52:51] Found bcftools - /usr/local/bin/bcftools
[06:52:51] Found samtools - /usr/local/bin/samtools
[06:52:51] Found java - /usr/local/bin/java
[06:52:51] Found snpEff - /usr/local/bin/snpEff
[06:52:51] Found samclip - /usr/local/bin/samclip
[06:52:51] Found seqtk - /usr/local/bin/seqtk
[06:52:51] Found parallel - /usr/local/bin/parallel
[06:52:51] Found freebayes - /usr/local/bin/freebayes
[06:52:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:51] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:51] Found gzip - /bin/gzip
[06:52:51] Found vt - /usr/local/bin/vt
[06:52:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:53:57] This is snippy 4.6.0Show full stderr[06:53:57] This is snippy 4.6.0
[06:53:57] Written by Torsten Seemann
[06:53:57] Obtained from https://github.com/tseemann/snippy
[06:53:57] Detected operating system: linux
[06:53:57] Enabling bundled linux tools.
[06:53:57] Found bwa - /usr/local/bin/bwa
[06:53:57] Found bcftools - /usr/local/bin/bcftools
[06:53:57] Found samtools - /usr/local/bin/samtools
[06:53:57] Found java - /usr/local/bin/java
[06:53:57] Found snpEff - /usr/local/bin/snpEff
[06:53:57] Found samclip - /usr/local/bin/samclip
[06:53:57] Found seqtk - /usr/local/bin/seqtk
[06:53:57] Found parallel - /usr/local/bin/parallel
[06:53:57] Found freebayes - /usr/local/bin/freebayes
[06:53:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:57] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:57] Found gzip - /bin/gzip
[06:53:57] Found vt - /usr/local/bin/vt
[06:53:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:56:12] This is snippy 4.6.0Show full stderr[06:56:12] This is snippy 4.6.0
[06:56:12] Written by Torsten Seemann
[06:56:12] Obtained from https://github.com/tseemann/snippy
[06:56:12] Detected operating system: linux
[06:56:12] Enabling bundled linux tools.
[06:56:12] Found bwa - /usr/local/bin/bwa
[06:56:12] Found bcftools - /usr/local/bin/bcftools
[06:56:12] Found samtools - /usr/local/bin/samtools
[06:56:12] Found java - /usr/local/bin/java
[06:56:12] Found snpEff - /usr/local/bin/snpEff
[06:56:12] Found samclip - /usr/local/bin/samclip
[06:56:12] Found seqtk - /usr/local/bin/seqtk
[06:56:12] Found parallel - /usr/local/bin/parallel
[06:56:12] Found freebayes - /usr/local/bin/freebayes
[06:56:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:56:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:56:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:56:12] Found vcfuniq - /usr/local/bin/vcfuniq
[06:56:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:56:12] Found gzip - /bin/gzip
[06:56:12] Found vt - /usr/local/bin/vt
[06:56:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:56:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:56:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:56:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:56:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:56:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:56:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:56:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:58:03] This is snippy 4.6.0Show full stderr[06:58:03] This is snippy 4.6.0
[06:58:03] Written by Torsten Seemann
[06:58:03] Obtained from https://github.com/tseemann/snippy
[06:58:03] Detected operating system: linux
[06:58:03] Enabling bundled linux tools.
[06:58:03] Found bwa - /usr/local/bin/bwa
[06:58:03] Found bcftools - /usr/local/bin/bcftools
[06:58:03] Found samtools - /usr/local/bin/samtools
[06:58:03] Found java - /usr/local/bin/java
[06:58:03] Found snpEff - /usr/local/bin/snpEff
[06:58:04] Found samclip - /usr/local/bin/samclip
[06:58:04] Found seqtk - /usr/local/bin/seqtk
[06:58:04] Found parallel - /usr/local/bin/parallel
[06:58:04] Found freebayes - /usr/local/bin/freebayes
[06:58:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:04] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:04] Found gzip - /bin/gzip
[06:58:04] Found vt - /usr/local/bin/vt
[06:58:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:58:28] This is snippy 4.6.0Show full stderr[06:58:28] This is snippy 4.6.0
[06:58:28] Written by Torsten Seemann
[06:58:28] Obtained from https://github.com/tseemann/snippy
[06:58:28] Detected operating system: linux
[06:58:28] Enabling bundled linux tools.
[06:58:28] Found bwa - /usr/local/bin/bwa
[06:58:28] Found bcftools - /usr/local/bin/bcftools
[06:58:28] Found samtools - /usr/local/bin/samtools
[06:58:28] Found java - /usr/local/bin/java
[06:58:28] Found snpEff - /usr/local/bin/snpEff
[06:58:28] Found samclip - /usr/local/bin/samclip
[06:58:28] Found seqtk - /usr/local/bin/seqtk
[06:58:28] Found parallel - /usr/local/bin/parallel
[06:58:28] Found freebayes - /usr/local/bin/freebayes
[06:58:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:28] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:28] Found gzip - /bin/gzip
[06:58:28] Found vt - /usr/local/bin/vt
[06:58:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [08:28:50] This is snippy 4.6.0Show full stderr[08:28:50] This is snippy 4.6.0
[08:28:50] Written by Torsten Seemann
[08:28:50] Obtained from https://github.com/tseemann/snippy
[08:28:50] Detected operating system: linux
[08:28:50] Enabling bundled linux tools.
[08:28:50] Found bwa - /usr/local/bin/bwa
[08:28:50] Found bcftools - /usr/local/bin/bcftools
[08:28:50] Found samtools - /usr/local/bin/samtools
[08:28:50] Found java - /usr/local/bin/java
[08:28:50] Found snpEff - /usr/local/bin/snpEff
[08:28:50] Found samclip - /usr/local/bin/samclip
[08:28:50] Found seqtk - /usr/local/bin/seqtk
[08:28:50] Found parallel - /usr/local/bin/parallel
[08:28:50] Found freebayes - /usr/local/bin/freebayes
[08:28:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:28:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:28:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:28:50] Found vcfuniq - /usr/local/bin/vcfuniq
[08:28:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:28:50] Found gzip - /bin/gzip
[08:28:50] Found vt - /usr/local/bin/vt
[08:28:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:28:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:28:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:28:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:28:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:28:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:28:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:28:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:55:37] This is snippy 4.6.0Show full stderr[06:55:37] This is snippy 4.6.0
[06:55:37] Written by Torsten Seemann
[06:55:37] Obtained from https://github.com/tseemann/snippy
[06:55:37] Detected operating system: linux
[06:55:37] Enabling bundled linux tools.
[06:55:37] Found bwa - /usr/local/bin/bwa
[06:55:37] Found bcftools - /usr/local/bin/bcftools
[06:55:37] Found samtools - /usr/local/bin/samtools
[06:55:37] Found java - /usr/local/bin/java
[06:55:37] Found snpEff - /usr/local/bin/snpEff
[06:55:37] Found samclip - /usr/local/bin/samclip
[06:55:37] Found seqtk - /usr/local/bin/seqtk
[06:55:37] Found parallel - /usr/local/bin/parallel
[06:55:37] Found freebayes - /usr/local/bin/freebayes
[06:55:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:37] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:37] Found gzip - /bin/gzip
[06:55:37] Found vt - /usr/local/bin/vt
[06:55:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:55:22] This is snippy 4.6.0Show full stderr[06:55:22] This is snippy 4.6.0
[06:55:22] Written by Torsten Seemann
[06:55:22] Obtained from https://github.com/tseemann/snippy
[06:55:22] Detected operating system: linux
[06:55:22] Enabling bundled linux tools.
[06:55:22] Found bwa - /usr/local/bin/bwa
[06:55:22] Found bcftools - /usr/local/bin/bcftools
[06:55:22] Found samtools - /usr/local/bin/samtools
[06:55:22] Found java - /usr/local/bin/java
[06:55:22] Found snpEff - /usr/local/bin/snpEff
[06:55:22] Found samclip - /usr/local/bin/samclip
[06:55:22] Found seqtk - /usr/local/bin/seqtk
[06:55:22] Found parallel - /usr/local/bin/parallel
[06:55:22] Found freebayes - /usr/local/bin/freebayes
[06:55:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:22] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:22] Found gzip - /bin/gzip
[06:55:22] Found vt - /usr/local/bin/vt
[06:55:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:39:11] This is snippy 4.6.0Show full stderr[07:39:11] This is snippy 4.6.0
[07:39:11] Written by Torsten Seemann
[07:39:11] Obtained from https://github.com/tseemann/snippy
[07:39:11] Detected operating system: linux
[07:39:11] Enabling bundled linux tools.
[07:39:11] Found bwa - /usr/local/bin/bwa
[07:39:11] Found bcftools - /usr/local/bin/bcftools
[07:39:11] Found samtools - /usr/local/bin/samtools
[07:39:11] Found java - /usr/local/bin/java
[07:39:11] Found snpEff - /usr/local/bin/snpEff
[07:39:11] Found samclip - /usr/local/bin/samclip
[07:39:11] Found seqtk - /usr/local/bin/seqtk
[07:39:11] Found parallel - /usr/local/bin/parallel
[07:39:11] Found freebayes - /usr/local/bin/freebayes
[07:39:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:39:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:39:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:39:11] Found vcfuniq - /usr/local/bin/vcfuniq
[07:39:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:39:11] Found gzip - /bin/gzip
[07:39:11] Found vt - /usr/local/bin/vt
[07:39:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:39:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:39:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:39:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:39:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:39:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:39:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:39:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:55:49] This is snippy 4.6.0Show full stderr[06:55:49] This is snippy 4.6.0
[06:55:49] Written by Torsten Seemann
[06:55:49] Obtained from https://github.com/tseemann/snippy
[06:55:49] Detected operating system: linux
[06:55:49] Enabling bundled linux tools.
[06:55:49] Found bwa - /usr/local/bin/bwa
[06:55:49] Found bcftools - /usr/local/bin/bcftools
[06:55:49] Found samtools - /usr/local/bin/samtools
[06:55:49] Found java - /usr/local/bin/java
[06:55:49] Found snpEff - /usr/local/bin/snpEff
[06:55:49] Found samclip - /usr/local/bin/samclip
[06:55:49] Found seqtk - /usr/local/bin/seqtk
[06:55:49] Found parallel - /usr/local/bin/parallel
[06:55:49] Found freebayes - /usr/local/bin/freebayes
[06:55:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:49] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:49] Found gzip - /bin/gzip
[06:55:49] Found vt - /usr/local/bin/vt
[06:55:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:55:58] This is snippy 4.6.0Show full stderr[06:55:58] This is snippy 4.6.0
[06:55:58] Written by Torsten Seemann
[06:55:58] Obtained from https://github.com/tseemann/snippy
[06:55:58] Detected operating system: linux
[06:55:58] Enabling bundled linux tools.
[06:55:58] Found bwa - /usr/local/bin/bwa
[06:55:58] Found bcftools - /usr/local/bin/bcftools
[06:55:58] Found samtools - /usr/local/bin/samtools
[06:55:58] Found java - /usr/local/bin/java
[06:55:58] Found snpEff - /usr/local/bin/snpEff
[06:55:58] Found samclip - /usr/local/bin/samclip
[06:55:58] Found seqtk - /usr/local/bin/seqtk
[06:55:58] Found parallel - /usr/local/bin/parallel
[06:55:58] Found freebayes - /usr/local/bin/freebayes
[06:55:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:58] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:58] Found gzip - /bin/gzip
[06:55:58] Found vt - /usr/local/bin/vt
[06:55:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:00:25] This is snippy 4.6.0Show full stderr[07:00:25] This is snippy 4.6.0
[07:00:25] Written by Torsten Seemann
[07:00:25] Obtained from https://github.com/tseemann/snippy
[07:00:25] Detected operating system: linux
[07:00:25] Enabling bundled linux tools.
[07:00:25] Found bwa - /usr/local/bin/bwa
[07:00:25] Found bcftools - /usr/local/bin/bcftools
[07:00:25] Found samtools - /usr/local/bin/samtools
[07:00:25] Found java - /usr/local/bin/java
[07:00:25] Found snpEff - /usr/local/bin/snpEff
[07:00:25] Found samclip - /usr/local/bin/samclip
[07:00:25] Found seqtk - /usr/local/bin/seqtk
[07:00:25] Found parallel - /usr/local/bin/parallel
[07:00:25] Found freebayes - /usr/local/bin/freebayes
[07:00:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:25] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:25] Found gzip - /bin/gzip
[07:00:25] Found vt - /usr/local/bin/vt
[07:00:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:59:55] This is snippy 4.6.0Show full stderr[06:59:55] This is snippy 4.6.0
[06:59:55] Written by Torsten Seemann
[06:59:55] Obtained from https://github.com/tseemann/snippy
[06:59:55] Detected operating system: linux
[06:59:55] Enabling bundled linux tools.
[06:59:55] Found bwa - /usr/local/bin/bwa
[06:59:55] Found bcftools - /usr/local/bin/bcftools
[06:59:55] Found samtools - /usr/local/bin/samtools
[06:59:55] Found java - /usr/local/bin/java
[06:59:55] Found snpEff - /usr/local/bin/snpEff
[06:59:55] Found samclip - /usr/local/bin/samclip
[06:59:55] Found seqtk - /usr/local/bin/seqtk
[06:59:55] Found parallel - /usr/local/bin/parallel
[06:59:55] Found freebayes - /usr/local/bin/freebayes
[06:59:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:55] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:55] Found gzip - /bin/gzip
[06:59:55] Found vt - /usr/local/bin/vt
[06:59:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:58:57] This is snippy 4.6.0Show full stderr[06:58:57] This is snippy 4.6.0
[06:58:57] Written by Torsten Seemann
[06:58:57] Obtained from https://github.com/tseemann/snippy
[06:58:57] Detected operating system: linux
[06:58:57] Enabling bundled linux tools.
[06:58:58] Found bwa - /usr/local/bin/bwa
[06:58:58] Found bcftools - /usr/local/bin/bcftools
[06:58:58] Found samtools - /usr/local/bin/samtools
[06:58:58] Found java - /usr/local/bin/java
[06:58:58] Found snpEff - /usr/local/bin/snpEff
[06:58:58] Found samclip - /usr/local/bin/samclip
[06:58:58] Found seqtk - /usr/local/bin/seqtk
[06:58:58] Found parallel - /usr/local/bin/parallel
[06:58:58] Found freebayes - /usr/local/bin/freebayes
[06:58:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:58] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:58] Found gzip - /bin/gzip
[06:58:58] Found vt - /usr/local/bin/vt
[06:58:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [06:59:43] This is snippy 4.6.0Show full stderr[06:59:43] This is snippy 4.6.0
[06:59:43] Written by Torsten Seemann
[06:59:43] Obtained from https://github.com/tseemann/snippy
[06:59:43] Detected operating system: linux
[06:59:43] Enabling bundled linux tools.
[06:59:43] Found bwa - /usr/local/bin/bwa
[06:59:43] Found bcftools - /usr/local/bin/bcftools
[06:59:43] Found samtools - /usr/local/bin/samtools
[06:59:43] Found java - /usr/local/bin/java
[06:59:43] Found snpEff - /usr/local/bin/snpEff
[06:59:43] Found samclip - /usr/local/bin/samclip
[06:59:43] Found seqtk - /usr/local/bin/seqtk
[06:59:43] Found parallel - /usr/local/bin/parallel
[06:59:43] Found freebayes - /usr/local/bin/freebayes
[06:59:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:43] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:43] Found gzip - /bin/gzip
[06:59:43] Found vt - /usr/local/bin/vt
[06:59:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:00:40] This is snippy 4.6.0Show full stderr[07:00:40] This is snippy 4.6.0
[07:00:40] Written by Torsten Seemann
[07:00:40] Obtained from https://github.com/tseemann/snippy
[07:00:40] Detected operating system: linux
[07:00:40] Enabling bundled linux tools.
[07:00:40] Found bwa - /usr/local/bin/bwa
[07:00:40] Found bcftools - /usr/local/bin/bcftools
[07:00:40] Found samtools - /usr/local/bin/samtools
[07:00:40] Found java - /usr/local/bin/java
[07:00:40] Found snpEff - /usr/local/bin/snpEff
[07:00:40] Found samclip - /usr/local/bin/samclip
[07:00:40] Found seqtk - /usr/local/bin/seqtk
[07:00:40] Found parallel - /usr/local/bin/parallel
[07:00:40] Found freebayes - /usr/local/bin/freebayes
[07:00:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:40] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:40] Found gzip - /bin/gzip
[07:00:40] Found vt - /usr/local/bin/vt
[07:00:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:02:44] This is snippy 4.6.0Show full stderr[07:02:44] This is snippy 4.6.0
[07:02:44] Written by Torsten Seemann
[07:02:44] Obtained from https://github.com/tseemann/snippy
[07:02:44] Detected operating system: linux
[07:02:44] Enabling bundled linux tools.
[07:02:44] Found bwa - /usr/local/bin/bwa
[07:02:44] Found bcftools - /usr/local/bin/bcftools
[07:02:44] Found samtools - /usr/local/bin/samtools
[07:02:44] Found java - /usr/local/bin/java
[07:02:44] Found snpEff - /usr/local/bin/snpEff
[07:02:44] Found samclip - /usr/local/bin/samclip
[07:02:44] Found seqtk - /usr/local/bin/seqtk
[07:02:44] Found parallel - /usr/local/bin/parallel
[07:02:44] Found freebayes - /usr/local/bin/freebayes
[07:02:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:02:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:02:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:02:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:02:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:02:44] Found gzip - /bin/gzip
[07:02:44] Found vt - /usr/local/bin/vt
[07:02:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:02:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:02:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:02:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:02:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:02:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:02:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:02:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:04:10] This is snippy 4.6.0Show full stderr[07:04:10] This is snippy 4.6.0
[07:04:10] Written by Torsten Seemann
[07:04:10] Obtained from https://github.com/tseemann/snippy
[07:04:10] Detected operating system: linux
[07:04:10] Enabling bundled linux tools.
[07:04:10] Found bwa - /usr/local/bin/bwa
[07:04:10] Found bcftools - /usr/local/bin/bcftools
[07:04:10] Found samtools - /usr/local/bin/samtools
[07:04:10] Found java - /usr/local/bin/java
[07:04:10] Found snpEff - /usr/local/bin/snpEff
[07:04:10] Found samclip - /usr/local/bin/samclip
[07:04:10] Found seqtk - /usr/local/bin/seqtk
[07:04:10] Found parallel - /usr/local/bin/parallel
[07:04:10] Found freebayes - /usr/local/bin/freebayes
[07:04:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:10] Found gzip - /bin/gzip
[07:04:10] Found vt - /usr/local/bin/vt
[07:04:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:05:07] This is snippy 4.6.0Show full stderr[07:05:07] This is snippy 4.6.0
[07:05:07] Written by Torsten Seemann
[07:05:07] Obtained from https://github.com/tseemann/snippy
[07:05:07] Detected operating system: linux
[07:05:07] Enabling bundled linux tools.
[07:05:07] Found bwa - /usr/local/bin/bwa
[07:05:07] Found bcftools - /usr/local/bin/bcftools
[07:05:07] Found samtools - /usr/local/bin/samtools
[07:05:07] Found java - /usr/local/bin/java
[07:05:07] Found snpEff - /usr/local/bin/snpEff
[07:05:07] Found samclip - /usr/local/bin/samclip
[07:05:07] Found seqtk - /usr/local/bin/seqtk
[07:05:07] Found parallel - /usr/local/bin/parallel
[07:05:07] Found freebayes - /usr/local/bin/freebayes
[07:05:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:07] Found gzip - /bin/gzip
[07:05:07] Found vt - /usr/local/bin/vt
[07:05:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:02:57] This is snippy 4.6.0Show full stderr[07:02:57] This is snippy 4.6.0
[07:02:57] Written by Torsten Seemann
[07:02:57] Obtained from https://github.com/tseemann/snippy
[07:02:57] Detected operating system: linux
[07:02:57] Enabling bundled linux tools.
[07:02:57] Found bwa - /usr/local/bin/bwa
[07:02:57] Found bcftools - /usr/local/bin/bcftools
[07:02:57] Found samtools - /usr/local/bin/samtools
[07:02:57] Found java - /usr/local/bin/java
[07:02:57] Found snpEff - /usr/local/bin/snpEff
[07:02:57] Found samclip - /usr/local/bin/samclip
[07:02:57] Found seqtk - /usr/local/bin/seqtk
[07:02:57] Found parallel - /usr/local/bin/parallel
[07:02:57] Found freebayes - /usr/local/bin/freebayes
[07:02:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:02:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:02:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:02:57] Found vcfuniq - /usr/local/bin/vcfuniq
[07:02:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:02:57] Found gzip - /bin/gzip
[07:02:57] Found vt - /usr/local/bin/vt
[07:02:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:02:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:02:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:02:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:02:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:02:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:02:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:02:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:03:10] This is snippy 4.6.0Show full stderr[07:03:10] This is snippy 4.6.0
[07:03:10] Written by Torsten Seemann
[07:03:10] Obtained from https://github.com/tseemann/snippy
[07:03:10] Detected operating system: linux
[07:03:10] Enabling bundled linux tools.
[07:03:10] Found bwa - /usr/local/bin/bwa
[07:03:10] Found bcftools - /usr/local/bin/bcftools
[07:03:10] Found samtools - /usr/local/bin/samtools
[07:03:10] Found java - /usr/local/bin/java
[07:03:10] Found snpEff - /usr/local/bin/snpEff
[07:03:10] Found samclip - /usr/local/bin/samclip
[07:03:10] Found seqtk - /usr/local/bin/seqtk
[07:03:10] Found parallel - /usr/local/bin/parallel
[07:03:10] Found freebayes - /usr/local/bin/freebayes
[07:03:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:10] Found gzip - /bin/gzip
[07:03:10] Found vt - /usr/local/bin/vt
[07:03:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [08:34:50] This is snippy 4.6.0Show full stderr[08:34:50] This is snippy 4.6.0
[08:34:50] Written by Torsten Seemann
[08:34:50] Obtained from https://github.com/tseemann/snippy
[08:34:50] Detected operating system: linux
[08:34:50] Enabling bundled linux tools.
[08:34:50] Found bwa - /usr/local/bin/bwa
[08:34:50] Found bcftools - /usr/local/bin/bcftools
[08:34:50] Found samtools - /usr/local/bin/samtools
[08:34:50] Found java - /usr/local/bin/java
[08:34:50] Found snpEff - /usr/local/bin/snpEff
[08:34:50] Found samclip - /usr/local/bin/samclip
[08:34:50] Found seqtk - /usr/local/bin/seqtk
[08:34:50] Found parallel - /usr/local/bin/parallel
[08:34:50] Found freebayes - /usr/local/bin/freebayes
[08:34:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:34:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:34:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:34:50] Found vcfuniq - /usr/local/bin/vcfuniq
[08:34:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:34:50] Found gzip - /bin/gzip
[08:34:50] Found vt - /usr/local/bin/vt
[08:34:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:34:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:34:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:34:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:34:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:34:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:34:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:34:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:03:55] This is snippy 4.6.0Show full stderr[07:03:55] This is snippy 4.6.0
[07:03:55] Written by Torsten Seemann
[07:03:55] Obtained from https://github.com/tseemann/snippy
[07:03:55] Detected operating system: linux
[07:03:55] Enabling bundled linux tools.
[07:03:55] Found bwa - /usr/local/bin/bwa
[07:03:55] Found bcftools - /usr/local/bin/bcftools
[07:03:55] Found samtools - /usr/local/bin/samtools
[07:03:55] Found java - /usr/local/bin/java
[07:03:55] Found snpEff - /usr/local/bin/snpEff
[07:03:55] Found samclip - /usr/local/bin/samclip
[07:03:55] Found seqtk - /usr/local/bin/seqtk
[07:03:55] Found parallel - /usr/local/bin/parallel
[07:03:55] Found freebayes - /usr/local/bin/freebayes
[07:03:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:55] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:55] Found gzip - /bin/gzip
[07:03:55] Found vt - /usr/local/bin/vt
[07:03:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:04:25] This is snippy 4.6.0Show full stderr[07:04:25] This is snippy 4.6.0
[07:04:25] Written by Torsten Seemann
[07:04:25] Obtained from https://github.com/tseemann/snippy
[07:04:25] Detected operating system: linux
[07:04:25] Enabling bundled linux tools.
[07:04:25] Found bwa - /usr/local/bin/bwa
[07:04:25] Found bcftools - /usr/local/bin/bcftools
[07:04:25] Found samtools - /usr/local/bin/samtools
[07:04:25] Found java - /usr/local/bin/java
[07:04:25] Found snpEff - /usr/local/bin/snpEff
[07:04:25] Found samclip - /usr/local/bin/samclip
[07:04:25] Found seqtk - /usr/local/bin/seqtk
[07:04:25] Found parallel - /usr/local/bin/parallel
[07:04:25] Found freebayes - /usr/local/bin/freebayes
[07:04:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:25] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:25] Found gzip - /bin/gzip
[07:04:25] Found vt - /usr/local/bin/vt
[07:04:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:05:32] This is snippy 4.6.0Show full stderr[07:05:32] This is snippy 4.6.0
[07:05:32] Written by Torsten Seemann
[07:05:32] Obtained from https://github.com/tseemann/snippy
[07:05:32] Detected operating system: linux
[07:05:32] Enabling bundled linux tools.
[07:05:32] Found bwa - /usr/local/bin/bwa
[07:05:32] Found bcftools - /usr/local/bin/bcftools
[07:05:32] Found samtools - /usr/local/bin/samtools
[07:05:32] Found java - /usr/local/bin/java
[07:05:32] Found snpEff - /usr/local/bin/snpEff
[07:05:32] Found samclip - /usr/local/bin/samclip
[07:05:32] Found seqtk - /usr/local/bin/seqtk
[07:05:32] Found parallel - /usr/local/bin/parallel
[07:05:32] Found freebayes - /usr/local/bin/freebayes
[07:05:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:32] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:32] Found gzip - /bin/gzip
[07:05:32] Found vt - /usr/local/bin/vt
[07:05:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:06:10] This is snippy 4.6.0Show full stderr[07:06:10] This is snippy 4.6.0
[07:06:10] Written by Torsten Seemann
[07:06:10] Obtained from https://github.com/tseemann/snippy
[07:06:10] Detected operating system: linux
[07:06:10] Enabling bundled linux tools.
[07:06:10] Found bwa - /usr/local/bin/bwa
[07:06:10] Found bcftools - /usr/local/bin/bcftools
[07:06:10] Found samtools - /usr/local/bin/samtools
[07:06:10] Found java - /usr/local/bin/java
[07:06:10] Found snpEff - /usr/local/bin/snpEff
[07:06:10] Found samclip - /usr/local/bin/samclip
[07:06:10] Found seqtk - /usr/local/bin/seqtk
[07:06:10] Found parallel - /usr/local/bin/parallel
[07:06:10] Found freebayes - /usr/local/bin/freebayes
[07:06:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:10] Found gzip - /bin/gzip
[07:06:10] Found vt - /usr/local/bin/vt
[07:06:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:06:32] This is snippy 4.6.0Show full stderr[07:06:32] This is snippy 4.6.0
[07:06:32] Written by Torsten Seemann
[07:06:32] Obtained from https://github.com/tseemann/snippy
[07:06:32] Detected operating system: linux
[07:06:32] Enabling bundled linux tools.
[07:06:32] Found bwa - /usr/local/bin/bwa
[07:06:32] Found bcftools - /usr/local/bin/bcftools
[07:06:32] Found samtools - /usr/local/bin/samtools
[07:06:32] Found java - /usr/local/bin/java
[07:06:32] Found snpEff - /usr/local/bin/snpEff
[07:06:32] Found samclip - /usr/local/bin/samclip
[07:06:32] Found seqtk - /usr/local/bin/seqtk
[07:06:32] Found parallel - /usr/local/bin/parallel
[07:06:32] Found freebayes - /usr/local/bin/freebayes
[07:06:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:32] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:32] Found gzip - /bin/gzip
[07:06:32] Found vt - /usr/local/bin/vt
[07:06:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [08:40:48] This is snippy 4.6.0Show full stderr[08:40:48] This is snippy 4.6.0
[08:40:48] Written by Torsten Seemann
[08:40:48] Obtained from https://github.com/tseemann/snippy
[08:40:48] Detected operating system: linux
[08:40:48] Enabling bundled linux tools.
[08:40:48] Found bwa - /usr/local/bin/bwa
[08:40:48] Found bcftools - /usr/local/bin/bcftools
[08:40:48] Found samtools - /usr/local/bin/samtools
[08:40:48] Found java - /usr/local/bin/java
[08:40:48] Found snpEff - /usr/local/bin/snpEff
[08:40:48] Found samclip - /usr/local/bin/samclip
[08:40:48] Found seqtk - /usr/local/bin/seqtk
[08:40:48] Found parallel - /usr/local/bin/parallel
[08:40:48] Found freebayes - /usr/local/bin/freebayes
[08:40:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:40:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:40:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:40:48] Found vcfuniq - /usr/local/bin/vcfuniq
[08:40:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:40:48] Found gzip - /bin/gzip
[08:40:48] Found vt - /usr/local/bin/vt
[08:40:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:40:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:40:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:40:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:40:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:40:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:40:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:40:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:07:38] This is snippy 4.6.0Show full stderr[07:07:38] This is snippy 4.6.0
[07:07:38] Written by Torsten Seemann
[07:07:38] Obtained from https://github.com/tseemann/snippy
[07:07:38] Detected operating system: linux
[07:07:38] Enabling bundled linux tools.
[07:07:38] Found bwa - /usr/local/bin/bwa
[07:07:38] Found bcftools - /usr/local/bin/bcftools
[07:07:38] Found samtools - /usr/local/bin/samtools
[07:07:38] Found java - /usr/local/bin/java
[07:07:38] Found snpEff - /usr/local/bin/snpEff
[07:07:38] Found samclip - /usr/local/bin/samclip
[07:07:38] Found seqtk - /usr/local/bin/seqtk
[07:07:38] Found parallel - /usr/local/bin/parallel
[07:07:38] Found freebayes - /usr/local/bin/freebayes
[07:07:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:38] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:38] Found gzip - /bin/gzip
[07:07:38] Found vt - /usr/local/bin/vt
[07:07:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:08:57] This is snippy 4.6.0Show full stderr[07:08:57] This is snippy 4.6.0
[07:08:57] Written by Torsten Seemann
[07:08:57] Obtained from https://github.com/tseemann/snippy
[07:08:57] Detected operating system: linux
[07:08:57] Enabling bundled linux tools.
[07:08:57] Found bwa - /usr/local/bin/bwa
[07:08:57] Found bcftools - /usr/local/bin/bcftools
[07:08:57] Found samtools - /usr/local/bin/samtools
[07:08:57] Found java - /usr/local/bin/java
[07:08:57] Found snpEff - /usr/local/bin/snpEff
[07:08:57] Found samclip - /usr/local/bin/samclip
[07:08:57] Found seqtk - /usr/local/bin/seqtk
[07:08:57] Found parallel - /usr/local/bin/parallel
[07:08:57] Found freebayes - /usr/local/bin/freebayes
[07:08:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:57] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:57] Found gzip - /bin/gzip
[07:08:57] Found vt - /usr/local/bin/vt
[07:08:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:06:59] This is snippy 4.6.0Show full stderr[07:06:59] This is snippy 4.6.0
[07:06:59] Written by Torsten Seemann
[07:06:59] Obtained from https://github.com/tseemann/snippy
[07:06:59] Detected operating system: linux
[07:06:59] Enabling bundled linux tools.
[07:06:59] Found bwa - /usr/local/bin/bwa
[07:06:59] Found bcftools - /usr/local/bin/bcftools
[07:06:59] Found samtools - /usr/local/bin/samtools
[07:06:59] Found java - /usr/local/bin/java
[07:06:59] Found snpEff - /usr/local/bin/snpEff
[07:06:59] Found samclip - /usr/local/bin/samclip
[07:06:59] Found seqtk - /usr/local/bin/seqtk
[07:06:59] Found parallel - /usr/local/bin/parallel
[07:06:59] Found freebayes - /usr/local/bin/freebayes
[07:06:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:59] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:59] Found gzip - /bin/gzip
[07:06:59] Found vt - /usr/local/bin/vt
[07:06:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:08:19] This is snippy 4.6.0Show full stderr[07:08:19] This is snippy 4.6.0
[07:08:19] Written by Torsten Seemann
[07:08:19] Obtained from https://github.com/tseemann/snippy
[07:08:19] Detected operating system: linux
[07:08:19] Enabling bundled linux tools.
[07:08:19] Found bwa - /usr/local/bin/bwa
[07:08:19] Found bcftools - /usr/local/bin/bcftools
[07:08:19] Found samtools - /usr/local/bin/samtools
[07:08:19] Found java - /usr/local/bin/java
[07:08:19] Found snpEff - /usr/local/bin/snpEff
[07:08:19] Found samclip - /usr/local/bin/samclip
[07:08:19] Found seqtk - /usr/local/bin/seqtk
[07:08:19] Found parallel - /usr/local/bin/parallel
[07:08:19] Found freebayes - /usr/local/bin/freebayes
[07:08:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:19] Found gzip - /bin/gzip
[07:08:19] Found vt - /usr/local/bin/vt
[07:08:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:09:11] This is snippy 4.6.0Show full stderr[07:09:11] This is snippy 4.6.0
[07:09:11] Written by Torsten Seemann
[07:09:11] Obtained from https://github.com/tseemann/snippy
[07:09:11] Detected operating system: linux
[07:09:11] Enabling bundled linux tools.
[07:09:11] Found bwa - /usr/local/bin/bwa
[07:09:11] Found bcftools - /usr/local/bin/bcftools
[07:09:11] Found samtools - /usr/local/bin/samtools
[07:09:11] Found java - /usr/local/bin/java
[07:09:11] Found snpEff - /usr/local/bin/snpEff
[07:09:11] Found samclip - /usr/local/bin/samclip
[07:09:11] Found seqtk - /usr/local/bin/seqtk
[07:09:11] Found parallel - /usr/local/bin/parallel
[07:09:11] Found freebayes - /usr/local/bin/freebayes
[07:09:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:09:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:09:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:09:11] Found vcfuniq - /usr/local/bin/vcfuniq
[07:09:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:09:11] Found gzip - /bin/gzip
[07:09:11] Found vt - /usr/local/bin/vt
[07:09:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:09:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:09:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:09:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:09:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:09:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:09:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:09:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:09:17] This is snippy 4.6.0Show full stderr[07:09:17] This is snippy 4.6.0
[07:09:17] Written by Torsten Seemann
[07:09:17] Obtained from https://github.com/tseemann/snippy
[07:09:17] Detected operating system: linux
[07:09:17] Enabling bundled linux tools.
[07:09:17] Found bwa - /usr/local/bin/bwa
[07:09:17] Found bcftools - /usr/local/bin/bcftools
[07:09:17] Found samtools - /usr/local/bin/samtools
[07:09:17] Found java - /usr/local/bin/java
[07:09:17] Found snpEff - /usr/local/bin/snpEff
[07:09:17] Found samclip - /usr/local/bin/samclip
[07:09:17] Found seqtk - /usr/local/bin/seqtk
[07:09:17] Found parallel - /usr/local/bin/parallel
[07:09:17] Found freebayes - /usr/local/bin/freebayes
[07:09:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:09:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:09:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:09:17] Found vcfuniq - /usr/local/bin/vcfuniq
[07:09:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:09:17] Found gzip - /bin/gzip
[07:09:17] Found vt - /usr/local/bin/vt
[07:09:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:09:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:09:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:09:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:09:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:09:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:09:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:09:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:15:35] This is snippy 4.6.0Show full stderr[07:15:35] This is snippy 4.6.0
[07:15:35] Written by Torsten Seemann
[07:15:35] Obtained from https://github.com/tseemann/snippy
[07:15:35] Detected operating system: linux
[07:15:35] Enabling bundled linux tools.
[07:15:35] Found bwa - /usr/local/bin/bwa
[07:15:35] Found bcftools - /usr/local/bin/bcftools
[07:15:35] Found samtools - /usr/local/bin/samtools
[07:15:35] Found java - /usr/local/bin/java
[07:15:35] Found snpEff - /usr/local/bin/snpEff
[07:15:35] Found samclip - /usr/local/bin/samclip
[07:15:35] Found seqtk - /usr/local/bin/seqtk
[07:15:35] Found parallel - /usr/local/bin/parallel
[07:15:35] Found freebayes - /usr/local/bin/freebayes
[07:15:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:15:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:15:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:15:35] Found vcfuniq - /usr/local/bin/vcfuniq
[07:15:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:15:35] Found gzip - /bin/gzip
[07:15:35] Found vt - /usr/local/bin/vt
[07:15:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:15:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:15:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:15:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:15:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:15:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:15:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:15:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:08:31] This is snippy 4.6.0Show full stderr[07:08:31] This is snippy 4.6.0
[07:08:31] Written by Torsten Seemann
[07:08:31] Obtained from https://github.com/tseemann/snippy
[07:08:31] Detected operating system: linux
[07:08:31] Enabling bundled linux tools.
[07:08:31] Found bwa - /usr/local/bin/bwa
[07:08:31] Found bcftools - /usr/local/bin/bcftools
[07:08:31] Found samtools - /usr/local/bin/samtools
[07:08:31] Found java - /usr/local/bin/java
[07:08:31] Found snpEff - /usr/local/bin/snpEff
[07:08:31] Found samclip - /usr/local/bin/samclip
[07:08:31] Found seqtk - /usr/local/bin/seqtk
[07:08:31] Found parallel - /usr/local/bin/parallel
[07:08:31] Found freebayes - /usr/local/bin/freebayes
[07:08:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:31] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:31] Found gzip - /bin/gzip
[07:08:31] Found vt - /usr/local/bin/vt
[07:08:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:08:44] This is snippy 4.6.0Show full stderr[07:08:44] This is snippy 4.6.0
[07:08:44] Written by Torsten Seemann
[07:08:44] Obtained from https://github.com/tseemann/snippy
[07:08:44] Detected operating system: linux
[07:08:44] Enabling bundled linux tools.
[07:08:44] Found bwa - /usr/local/bin/bwa
[07:08:44] Found bcftools - /usr/local/bin/bcftools
[07:08:44] Found samtools - /usr/local/bin/samtools
[07:08:44] Found java - /usr/local/bin/java
[07:08:44] Found snpEff - /usr/local/bin/snpEff
[07:08:44] Found samclip - /usr/local/bin/samclip
[07:08:44] Found seqtk - /usr/local/bin/seqtk
[07:08:44] Found parallel - /usr/local/bin/parallel
[07:08:44] Found freebayes - /usr/local/bin/freebayes
[07:08:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:44] Found gzip - /bin/gzip
[07:08:44] Found vt - /usr/local/bin/vt
[07:08:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:09:32] This is snippy 4.6.0Show full stderr[07:09:32] This is snippy 4.6.0
[07:09:32] Written by Torsten Seemann
[07:09:32] Obtained from https://github.com/tseemann/snippy
[07:09:32] Detected operating system: linux
[07:09:32] Enabling bundled linux tools.
[07:09:32] Found bwa - /usr/local/bin/bwa
[07:09:32] Found bcftools - /usr/local/bin/bcftools
[07:09:32] Found samtools - /usr/local/bin/samtools
[07:09:32] Found java - /usr/local/bin/java
[07:09:32] Found snpEff - /usr/local/bin/snpEff
[07:09:32] Found samclip - /usr/local/bin/samclip
[07:09:32] Found seqtk - /usr/local/bin/seqtk
[07:09:32] Found parallel - /usr/local/bin/parallel
[07:09:32] Found freebayes - /usr/local/bin/freebayes
[07:09:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:09:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:09:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:09:32] Found vcfuniq - /usr/local/bin/vcfuniq
[07:09:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:09:32] Found gzip - /bin/gzip
[07:09:32] Found vt - /usr/local/bin/vt
[07:09:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:09:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:09:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:09:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:09:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:09:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:09:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:09:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:05:51] This is snippy 4.6.0Show full stderr[07:05:51] This is snippy 4.6.0
[07:05:51] Written by Torsten Seemann
[07:05:51] Obtained from https://github.com/tseemann/snippy
[07:05:51] Detected operating system: linux
[07:05:51] Enabling bundled linux tools.
[07:05:51] Found bwa - /usr/local/bin/bwa
[07:05:51] Found bcftools - /usr/local/bin/bcftools
[07:05:51] Found samtools - /usr/local/bin/samtools
[07:05:51] Found java - /usr/local/bin/java
[07:05:51] Found snpEff - /usr/local/bin/snpEff
[07:05:51] Found samclip - /usr/local/bin/samclip
[07:05:51] Found seqtk - /usr/local/bin/seqtk
[07:05:51] Found parallel - /usr/local/bin/parallel
[07:05:51] Found freebayes - /usr/local/bin/freebayes
[07:05:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:51] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:51] Found gzip - /bin/gzip
[07:05:51] Found vt - /usr/local/bin/vt
[07:05:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:06:44] This is snippy 4.6.0Show full stderr[07:06:44] This is snippy 4.6.0
[07:06:44] Written by Torsten Seemann
[07:06:44] Obtained from https://github.com/tseemann/snippy
[07:06:44] Detected operating system: linux
[07:06:44] Enabling bundled linux tools.
[07:06:44] Found bwa - /usr/local/bin/bwa
[07:06:44] Found bcftools - /usr/local/bin/bcftools
[07:06:44] Found samtools - /usr/local/bin/samtools
[07:06:44] Found java - /usr/local/bin/java
[07:06:44] Found snpEff - /usr/local/bin/snpEff
[07:06:44] Found samclip - /usr/local/bin/samclip
[07:06:44] Found seqtk - /usr/local/bin/seqtk
[07:06:44] Found parallel - /usr/local/bin/parallel
[07:06:44] Found freebayes - /usr/local/bin/freebayes
[07:06:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:44] Found gzip - /bin/gzip
[07:06:44] Found vt - /usr/local/bin/vt
[07:06:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:11:49] This is snippy 4.6.0Show full stderr[07:11:49] This is snippy 4.6.0
[07:11:49] Written by Torsten Seemann
[07:11:49] Obtained from https://github.com/tseemann/snippy
[07:11:49] Detected operating system: linux
[07:11:49] Enabling bundled linux tools.
[07:11:49] Found bwa - /usr/local/bin/bwa
[07:11:49] Found bcftools - /usr/local/bin/bcftools
[07:11:49] Found samtools - /usr/local/bin/samtools
[07:11:49] Found java - /usr/local/bin/java
[07:11:49] Found snpEff - /usr/local/bin/snpEff
[07:11:49] Found samclip - /usr/local/bin/samclip
[07:11:49] Found seqtk - /usr/local/bin/seqtk
[07:11:49] Found parallel - /usr/local/bin/parallel
[07:11:49] Found freebayes - /usr/local/bin/freebayes
[07:11:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:11:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:11:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:11:49] Found vcfuniq - /usr/local/bin/vcfuniq
[07:11:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:11:49] Found gzip - /bin/gzip
[07:11:49] Found vt - /usr/local/bin/vt
[07:11:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:11:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:11:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:11:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:11:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:11:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:11:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:11:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:12:06] This is snippy 4.6.0Show full stderr[07:12:06] This is snippy 4.6.0
[07:12:06] Written by Torsten Seemann
[07:12:06] Obtained from https://github.com/tseemann/snippy
[07:12:06] Detected operating system: linux
[07:12:06] Enabling bundled linux tools.
[07:12:06] Found bwa - /usr/local/bin/bwa
[07:12:06] Found bcftools - /usr/local/bin/bcftools
[07:12:06] Found samtools - /usr/local/bin/samtools
[07:12:06] Found java - /usr/local/bin/java
[07:12:06] Found snpEff - /usr/local/bin/snpEff
[07:12:06] Found samclip - /usr/local/bin/samclip
[07:12:06] Found seqtk - /usr/local/bin/seqtk
[07:12:06] Found parallel - /usr/local/bin/parallel
[07:12:06] Found freebayes - /usr/local/bin/freebayes
[07:12:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:12:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:12:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:12:06] Found vcfuniq - /usr/local/bin/vcfuniq
[07:12:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:12:06] Found gzip - /bin/gzip
[07:12:06] Found vt - /usr/local/bin/vt
[07:12:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:12:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:12:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:12:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:12:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:12:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:12:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:12:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:12:17] This is snippy 4.6.0Show full stderr[07:12:17] This is snippy 4.6.0
[07:12:17] Written by Torsten Seemann
[07:12:17] Obtained from https://github.com/tseemann/snippy
[07:12:17] Detected operating system: linux
[07:12:17] Enabling bundled linux tools.
[07:12:17] Found bwa - /usr/local/bin/bwa
[07:12:17] Found bcftools - /usr/local/bin/bcftools
[07:12:17] Found samtools - /usr/local/bin/samtools
[07:12:17] Found java - /usr/local/bin/java
[07:12:17] Found snpEff - /usr/local/bin/snpEff
[07:12:17] Found samclip - /usr/local/bin/samclip
[07:12:17] Found seqtk - /usr/local/bin/seqtk
[07:12:17] Found parallel - /usr/local/bin/parallel
[07:12:17] Found freebayes - /usr/local/bin/freebayes
[07:12:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:12:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:12:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:12:17] Found vcfuniq - /usr/local/bin/vcfuniq
[07:12:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:12:17] Found gzip - /bin/gzip
[07:12:17] Found vt - /usr/local/bin/vt
[07:12:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:12:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:12:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:12:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:12:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:12:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:12:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:12:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:12:58] This is snippy 4.6.0Show full stderr[07:12:58] This is snippy 4.6.0
[07:12:58] Written by Torsten Seemann
[07:12:58] Obtained from https://github.com/tseemann/snippy
[07:12:58] Detected operating system: linux
[07:12:58] Enabling bundled linux tools.
[07:12:58] Found bwa - /usr/local/bin/bwa
[07:12:58] Found bcftools - /usr/local/bin/bcftools
[07:12:58] Found samtools - /usr/local/bin/samtools
[07:12:58] Found java - /usr/local/bin/java
[07:12:58] Found snpEff - /usr/local/bin/snpEff
[07:12:58] Found samclip - /usr/local/bin/samclip
[07:12:58] Found seqtk - /usr/local/bin/seqtk
[07:12:58] Found parallel - /usr/local/bin/parallel
[07:12:58] Found freebayes - /usr/local/bin/freebayes
[07:12:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:12:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:12:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:12:58] Found vcfuniq - /usr/local/bin/vcfuniq
[07:12:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:12:59] Found gzip - /bin/gzip
[07:12:59] Found vt - /usr/local/bin/vt
[07:12:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:12:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:12:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:12:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:12:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:12:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:12:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:12:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:11:38] This is snippy 4.6.0Show full stderr[07:11:38] This is snippy 4.6.0
[07:11:38] Written by Torsten Seemann
[07:11:38] Obtained from https://github.com/tseemann/snippy
[07:11:38] Detected operating system: linux
[07:11:38] Enabling bundled linux tools.
[07:11:38] Found bwa - /usr/local/bin/bwa
[07:11:38] Found bcftools - /usr/local/bin/bcftools
[07:11:38] Found samtools - /usr/local/bin/samtools
[07:11:38] Found java - /usr/local/bin/java
[07:11:38] Found snpEff - /usr/local/bin/snpEff
[07:11:38] Found samclip - /usr/local/bin/samclip
[07:11:38] Found seqtk - /usr/local/bin/seqtk
[07:11:38] Found parallel - /usr/local/bin/parallel
[07:11:38] Found freebayes - /usr/local/bin/freebayes
[07:11:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:11:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:11:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:11:38] Found vcfuniq - /usr/local/bin/vcfuniq
[07:11:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:11:38] Found gzip - /bin/gzip
[07:11:38] Found vt - /usr/local/bin/vt
[07:11:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:11:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:11:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:11:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:11:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:11:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:11:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:11:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:12:03] This is snippy 4.6.0Show full stderr[07:12:03] This is snippy 4.6.0
[07:12:03] Written by Torsten Seemann
[07:12:03] Obtained from https://github.com/tseemann/snippy
[07:12:03] Detected operating system: linux
[07:12:03] Enabling bundled linux tools.
[07:12:03] Found bwa - /usr/local/bin/bwa
[07:12:03] Found bcftools - /usr/local/bin/bcftools
[07:12:03] Found samtools - /usr/local/bin/samtools
[07:12:03] Found java - /usr/local/bin/java
[07:12:03] Found snpEff - /usr/local/bin/snpEff
[07:12:03] Found samclip - /usr/local/bin/samclip
[07:12:03] Found seqtk - /usr/local/bin/seqtk
[07:12:03] Found parallel - /usr/local/bin/parallel
[07:12:03] Found freebayes - /usr/local/bin/freebayes
[07:12:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:12:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:12:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:12:03] Found vcfuniq - /usr/local/bin/vcfuniq
[07:12:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:12:03] Found gzip - /bin/gzip
[07:12:03] Found vt - /usr/local/bin/vt
[07:12:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:12:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:12:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:12:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:12:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:12:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:12:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:12:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:11:53] This is snippy 4.6.0Show full stderr[07:11:53] This is snippy 4.6.0
[07:11:53] Written by Torsten Seemann
[07:11:53] Obtained from https://github.com/tseemann/snippy
[07:11:53] Detected operating system: linux
[07:11:53] Enabling bundled linux tools.
[07:11:53] Found bwa - /usr/local/bin/bwa
[07:11:53] Found bcftools - /usr/local/bin/bcftools
[07:11:53] Found samtools - /usr/local/bin/samtools
[07:11:53] Found java - /usr/local/bin/java
[07:11:53] Found snpEff - /usr/local/bin/snpEff
[07:11:53] Found samclip - /usr/local/bin/samclip
[07:11:53] Found seqtk - /usr/local/bin/seqtk
[07:11:53] Found parallel - /usr/local/bin/parallel
[07:11:53] Found freebayes - /usr/local/bin/freebayes
[07:11:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:11:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:11:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:11:53] Found vcfuniq - /usr/local/bin/vcfuniq
[07:11:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:11:53] Found gzip - /bin/gzip
[07:11:53] Found vt - /usr/local/bin/vt
[07:11:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:11:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:11:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:11:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:11:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:11:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:11:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:11:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:12:46] This is snippy 4.6.0Show full stderr[07:12:46] This is snippy 4.6.0
[07:12:46] Written by Torsten Seemann
[07:12:46] Obtained from https://github.com/tseemann/snippy
[07:12:46] Detected operating system: linux
[07:12:46] Enabling bundled linux tools.
[07:12:46] Found bwa - /usr/local/bin/bwa
[07:12:46] Found bcftools - /usr/local/bin/bcftools
[07:12:46] Found samtools - /usr/local/bin/samtools
[07:12:46] Found java - /usr/local/bin/java
[07:12:46] Found snpEff - /usr/local/bin/snpEff
[07:12:46] Found samclip - /usr/local/bin/samclip
[07:12:46] Found seqtk - /usr/local/bin/seqtk
[07:12:46] Found parallel - /usr/local/bin/parallel
[07:12:46] Found freebayes - /usr/local/bin/freebayes
[07:12:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:12:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:12:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:12:46] Found vcfuniq - /usr/local/bin/vcfuniq
[07:12:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:12:46] Found gzip - /bin/gzip
[07:12:46] Found vt - /usr/local/bin/vt
[07:12:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:12:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:12:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:12:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:12:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:12:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:12:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:12:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:13:12] This is snippy 4.6.0Show full stderr[07:13:12] This is snippy 4.6.0
[07:13:12] Written by Torsten Seemann
[07:13:12] Obtained from https://github.com/tseemann/snippy
[07:13:12] Detected operating system: linux
[07:13:12] Enabling bundled linux tools.
[07:13:12] Found bwa - /usr/local/bin/bwa
[07:13:12] Found bcftools - /usr/local/bin/bcftools
[07:13:12] Found samtools - /usr/local/bin/samtools
[07:13:12] Found java - /usr/local/bin/java
[07:13:12] Found snpEff - /usr/local/bin/snpEff
[07:13:12] Found samclip - /usr/local/bin/samclip
[07:13:12] Found seqtk - /usr/local/bin/seqtk
[07:13:12] Found parallel - /usr/local/bin/parallel
[07:13:12] Found freebayes - /usr/local/bin/freebayes
[07:13:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:13:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:13:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:13:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:13:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:13:13] Found gzip - /bin/gzip
[07:13:13] Found vt - /usr/local/bin/vt
[07:13:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:13:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:13:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:13:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:13:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:13:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:13:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:13:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:16:02] This is snippy 4.6.0Show full stderr[07:16:02] This is snippy 4.6.0
[07:16:02] Written by Torsten Seemann
[07:16:02] Obtained from https://github.com/tseemann/snippy
[07:16:02] Detected operating system: linux
[07:16:02] Enabling bundled linux tools.
[07:16:02] Found bwa - /usr/local/bin/bwa
[07:16:02] Found bcftools - /usr/local/bin/bcftools
[07:16:02] Found samtools - /usr/local/bin/samtools
[07:16:02] Found java - /usr/local/bin/java
[07:16:02] Found snpEff - /usr/local/bin/snpEff
[07:16:02] Found samclip - /usr/local/bin/samclip
[07:16:02] Found seqtk - /usr/local/bin/seqtk
[07:16:02] Found parallel - /usr/local/bin/parallel
[07:16:02] Found freebayes - /usr/local/bin/freebayes
[07:16:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:16:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:16:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:16:02] Found vcfuniq - /usr/local/bin/vcfuniq
[07:16:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:16:02] Found gzip - /bin/gzip
[07:16:02] Found vt - /usr/local/bin/vt
[07:16:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:16:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:16:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:16:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:16:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:16:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:16:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:16:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:15:49] This is snippy 4.6.0Show full stderr[07:15:49] This is snippy 4.6.0
[07:15:49] Written by Torsten Seemann
[07:15:49] Obtained from https://github.com/tseemann/snippy
[07:15:49] Detected operating system: linux
[07:15:49] Enabling bundled linux tools.
[07:15:49] Found bwa - /usr/local/bin/bwa
[07:15:49] Found bcftools - /usr/local/bin/bcftools
[07:15:49] Found samtools - /usr/local/bin/samtools
[07:15:49] Found java - /usr/local/bin/java
[07:15:49] Found snpEff - /usr/local/bin/snpEff
[07:15:49] Found samclip - /usr/local/bin/samclip
[07:15:49] Found seqtk - /usr/local/bin/seqtk
[07:15:49] Found parallel - /usr/local/bin/parallel
[07:15:49] Found freebayes - /usr/local/bin/freebayes
[07:15:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:15:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:15:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:15:49] Found vcfuniq - /usr/local/bin/vcfuniq
[07:15:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:15:49] Found gzip - /bin/gzip
[07:15:49] Found vt - /usr/local/bin/vt
[07:15:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:15:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:15:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:15:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:15:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:15:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:15:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:15:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:26:09] This is snippy 4.6.0Show full stderr[07:26:09] This is snippy 4.6.0
[07:26:09] Written by Torsten Seemann
[07:26:09] Obtained from https://github.com/tseemann/snippy
[07:26:09] Detected operating system: linux
[07:26:09] Enabling bundled linux tools.
[07:26:09] Found bwa - /usr/local/bin/bwa
[07:26:09] Found bcftools - /usr/local/bin/bcftools
[07:26:09] Found samtools - /usr/local/bin/samtools
[07:26:09] Found java - /usr/local/bin/java
[07:26:09] Found snpEff - /usr/local/bin/snpEff
[07:26:09] Found samclip - /usr/local/bin/samclip
[07:26:09] Found seqtk - /usr/local/bin/seqtk
[07:26:09] Found parallel - /usr/local/bin/parallel
[07:26:09] Found freebayes - /usr/local/bin/freebayes
[07:26:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:26:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:26:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:26:09] Found vcfuniq - /usr/local/bin/vcfuniq
[07:26:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:26:09] Found gzip - /bin/gzip
[07:26:09] Found vt - /usr/local/bin/vt
[07:26:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:26:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:26:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:26:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:26:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:26:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:26:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:26:10] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:26:10] Treating reference as 'fasta' format.
[07:26:10] Will use 1 CPU cores.
[07:26:10] Using read file: /corral4/main/objects/b/9/3/dataset_b931e0c8-c97a-491e-9665-7515b51f803c.dat
[07:26:10] Creating folder: BVBRC_genome_sequence___2025_10_25T135701_613_fasta
[07:26:10] Changing working directory: BVBRC_genome_sequence___2025_10_25T135701_613_fasta
[07:26:10] Creating reference folder: reference
[07:26:10] Extracting FASTA and GFF from reference.
[07:26:10] Wrote 1 sequences to ref.fa
[07:26:10] Wrote 0 features to ref.gff
[07:26:10] Shredding /corral4/main/objects/b/9/3/dataset_b931e0c8-c97a-491e-9665-7515b51f803c.dat into pseudo-reads
[07:26:12] Wrote 219280 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:26:12] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[07:26:12] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135701_613_fasta
[07:26:12] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:26:13] Running: bwa index reference/ref.fa 2>> snps.log
[07:26:14] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[07:26:14] Running: ln -sf reference/ref.fa . 2>> snps.log
[07:26:14] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[07:26:14] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[07:26:14] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135701_613_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135701_613_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/263/72263194/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/263/72263194/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/263/72263194/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::process] read 19280 sequences (4820000 bp)...
[M::mem_proc |
| 2 | [07:26:12] This is snippy 4.6.0Show full stderr[07:26:12] This is snippy 4.6.0
[07:26:12] Written by Torsten Seemann
[07:26:12] Obtained from https://github.com/tseemann/snippy
[07:26:12] Detected operating system: linux
[07:26:12] Enabling bundled linux tools.
[07:26:12] Found bwa - /usr/local/bin/bwa
[07:26:12] Found bcftools - /usr/local/bin/bcftools
[07:26:12] Found samtools - /usr/local/bin/samtools
[07:26:12] Found java - /usr/local/bin/java
[07:26:12] Found snpEff - /usr/local/bin/snpEff
[07:26:12] Found samclip - /usr/local/bin/samclip
[07:26:12] Found seqtk - /usr/local/bin/seqtk
[07:26:12] Found parallel - /usr/local/bin/parallel
[07:26:12] Found freebayes - /usr/local/bin/freebayes
[07:26:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:26:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:26:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:26:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:26:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:26:13] Found gzip - /bin/gzip
[07:26:13] Found vt - /usr/local/bin/vt
[07:26:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:26:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:26:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:26:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:26:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:26:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:26:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:26:13] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:26:13] Treating reference as 'fasta' format.
[07:26:13] Will use 1 CPU cores.
[07:26:13] Using read file: /corral4/main/objects/f/9/1/dataset_f91c1dae-8edf-47ef-85e8-e7216580cbc0.dat
[07:26:13] Creating folder: BVBRC_genome_sequence___2025_10_25T135718_903_fasta
[07:26:13] Changing working directory: BVBRC_genome_sequence___2025_10_25T135718_903_fasta
[07:26:13] Creating reference folder: reference
[07:26:13] Extracting FASTA and GFF from reference.
[07:26:13] Wrote 1 sequences to ref.fa
[07:26:13] Wrote 0 features to ref.gff
[07:26:13] Shredding /corral4/main/objects/f/9/1/dataset_f91c1dae-8edf-47ef-85e8-e7216580cbc0.dat into pseudo-reads
[07:26:16] Wrote 221700 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:26:16] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[07:26:16] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135718_903_fasta
[07:26:16] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:26:16] Running: bwa index reference/ref.fa 2>> snps.log
[07:26:17] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[07:26:17] Running: ln -sf reference/ref.fa . 2>> snps.log
[07:26:17] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[07:26:17] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[07:26:17] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135718_903_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135718_903_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/263/72263198/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/263/72263198/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/263/72263198/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::process] read 21700 sequences (5425000 bp)...
[M::mem_proc |
| 2 | [07:28:56] This is snippy 4.6.0Show full stderr[07:28:56] This is snippy 4.6.0
[07:28:56] Written by Torsten Seemann
[07:28:56] Obtained from https://github.com/tseemann/snippy
[07:28:56] Detected operating system: linux
[07:28:56] Enabling bundled linux tools.
[07:28:56] Found bwa - /usr/local/bin/bwa
[07:28:56] Found bcftools - /usr/local/bin/bcftools
[07:28:56] Found samtools - /usr/local/bin/samtools
[07:28:56] Found java - /usr/local/bin/java
[07:28:56] Found snpEff - /usr/local/bin/snpEff
[07:28:56] Found samclip - /usr/local/bin/samclip
[07:28:56] Found seqtk - /usr/local/bin/seqtk
[07:28:56] Found parallel - /usr/local/bin/parallel
[07:28:56] Found freebayes - /usr/local/bin/freebayes
[07:28:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:28:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:28:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:28:56] Found vcfuniq - /usr/local/bin/vcfuniq
[07:28:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:28:56] Found gzip - /bin/gzip
[07:28:56] Found vt - /usr/local/bin/vt
[07:28:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:28:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:28:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:28:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:28:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:28:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:28:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:28:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:29:25] This is snippy 4.6.0Show full stderr[07:29:25] This is snippy 4.6.0
[07:29:25] Written by Torsten Seemann
[07:29:25] Obtained from https://github.com/tseemann/snippy
[07:29:25] Detected operating system: linux
[07:29:25] Enabling bundled linux tools.
[07:29:25] Found bwa - /usr/local/bin/bwa
[07:29:25] Found bcftools - /usr/local/bin/bcftools
[07:29:25] Found samtools - /usr/local/bin/samtools
[07:29:25] Found java - /usr/local/bin/java
[07:29:25] Found snpEff - /usr/local/bin/snpEff
[07:29:25] Found samclip - /usr/local/bin/samclip
[07:29:25] Found seqtk - /usr/local/bin/seqtk
[07:29:25] Found parallel - /usr/local/bin/parallel
[07:29:25] Found freebayes - /usr/local/bin/freebayes
[07:29:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:29:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:29:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:29:25] Found vcfuniq - /usr/local/bin/vcfuniq
[07:29:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:29:25] Found gzip - /bin/gzip
[07:29:25] Found vt - /usr/local/bin/vt
[07:29:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:29:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:29:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:29:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:29:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:29:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:29:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:29:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:30:40] This is snippy 4.6.0Show full stderr[07:30:40] This is snippy 4.6.0
[07:30:40] Written by Torsten Seemann
[07:30:40] Obtained from https://github.com/tseemann/snippy
[07:30:40] Detected operating system: linux
[07:30:40] Enabling bundled linux tools.
[07:30:40] Found bwa - /usr/local/bin/bwa
[07:30:40] Found bcftools - /usr/local/bin/bcftools
[07:30:40] Found samtools - /usr/local/bin/samtools
[07:30:40] Found java - /usr/local/bin/java
[07:30:40] Found snpEff - /usr/local/bin/snpEff
[07:30:40] Found samclip - /usr/local/bin/samclip
[07:30:40] Found seqtk - /usr/local/bin/seqtk
[07:30:40] Found parallel - /usr/local/bin/parallel
[07:30:40] Found freebayes - /usr/local/bin/freebayes
[07:30:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:30:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:30:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:30:40] Found vcfuniq - /usr/local/bin/vcfuniq
[07:30:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:30:40] Found gzip - /bin/gzip
[07:30:40] Found vt - /usr/local/bin/vt
[07:30:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:30:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:30:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:30:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:30:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:30:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:30:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:30:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:30:57] This is snippy 4.6.0Show full stderr[07:30:57] This is snippy 4.6.0
[07:30:57] Written by Torsten Seemann
[07:30:57] Obtained from https://github.com/tseemann/snippy
[07:30:57] Detected operating system: linux
[07:30:57] Enabling bundled linux tools.
[07:30:57] Found bwa - /usr/local/bin/bwa
[07:30:57] Found bcftools - /usr/local/bin/bcftools
[07:30:57] Found samtools - /usr/local/bin/samtools
[07:30:57] Found java - /usr/local/bin/java
[07:30:57] Found snpEff - /usr/local/bin/snpEff
[07:30:57] Found samclip - /usr/local/bin/samclip
[07:30:57] Found seqtk - /usr/local/bin/seqtk
[07:30:57] Found parallel - /usr/local/bin/parallel
[07:30:57] Found freebayes - /usr/local/bin/freebayes
[07:30:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:30:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:30:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:30:57] Found vcfuniq - /usr/local/bin/vcfuniq
[07:30:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:30:57] Found gzip - /bin/gzip
[07:30:57] Found vt - /usr/local/bin/vt
[07:30:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:30:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:30:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:30:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:30:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:30:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:30:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:30:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:31:10] This is snippy 4.6.0Show full stderr[07:31:10] This is snippy 4.6.0
[07:31:10] Written by Torsten Seemann
[07:31:10] Obtained from https://github.com/tseemann/snippy
[07:31:10] Detected operating system: linux
[07:31:10] Enabling bundled linux tools.
[07:31:10] Found bwa - /usr/local/bin/bwa
[07:31:10] Found bcftools - /usr/local/bin/bcftools
[07:31:10] Found samtools - /usr/local/bin/samtools
[07:31:10] Found java - /usr/local/bin/java
[07:31:10] Found snpEff - /usr/local/bin/snpEff
[07:31:10] Found samclip - /usr/local/bin/samclip
[07:31:10] Found seqtk - /usr/local/bin/seqtk
[07:31:10] Found parallel - /usr/local/bin/parallel
[07:31:10] Found freebayes - /usr/local/bin/freebayes
[07:31:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:31:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:31:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:31:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:31:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:31:10] Found gzip - /bin/gzip
[07:31:10] Found vt - /usr/local/bin/vt
[07:31:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:31:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:31:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:31:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:31:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:31:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:31:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:31:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:28:41] This is snippy 4.6.0Show full stderr[07:28:41] This is snippy 4.6.0
[07:28:41] Written by Torsten Seemann
[07:28:41] Obtained from https://github.com/tseemann/snippy
[07:28:41] Detected operating system: linux
[07:28:41] Enabling bundled linux tools.
[07:28:41] Found bwa - /usr/local/bin/bwa
[07:28:41] Found bcftools - /usr/local/bin/bcftools
[07:28:41] Found samtools - /usr/local/bin/samtools
[07:28:41] Found java - /usr/local/bin/java
[07:28:41] Found snpEff - /usr/local/bin/snpEff
[07:28:41] Found samclip - /usr/local/bin/samclip
[07:28:41] Found seqtk - /usr/local/bin/seqtk
[07:28:41] Found parallel - /usr/local/bin/parallel
[07:28:41] Found freebayes - /usr/local/bin/freebayes
[07:28:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:28:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:28:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:28:41] Found vcfuniq - /usr/local/bin/vcfuniq
[07:28:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:28:41] Found gzip - /bin/gzip
[07:28:41] Found vt - /usr/local/bin/vt
[07:28:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:28:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:28:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:28:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:28:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:28:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:28:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:28:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:28:16] This is snippy 4.6.0Show full stderr[07:28:16] This is snippy 4.6.0
[07:28:16] Written by Torsten Seemann
[07:28:16] Obtained from https://github.com/tseemann/snippy
[07:28:16] Detected operating system: linux
[07:28:16] Enabling bundled linux tools.
[07:28:16] Found bwa - /usr/local/bin/bwa
[07:28:16] Found bcftools - /usr/local/bin/bcftools
[07:28:16] Found samtools - /usr/local/bin/samtools
[07:28:16] Found java - /usr/local/bin/java
[07:28:16] Found snpEff - /usr/local/bin/snpEff
[07:28:16] Found samclip - /usr/local/bin/samclip
[07:28:16] Found seqtk - /usr/local/bin/seqtk
[07:28:16] Found parallel - /usr/local/bin/parallel
[07:28:16] Found freebayes - /usr/local/bin/freebayes
[07:28:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:28:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:28:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:28:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:28:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:28:16] Found gzip - /bin/gzip
[07:28:16] Found vt - /usr/local/bin/vt
[07:28:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:28:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:28:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:28:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:28:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:28:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:28:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:28:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:28:32] This is snippy 4.6.0Show full stderr[07:28:32] This is snippy 4.6.0
[07:28:32] Written by Torsten Seemann
[07:28:32] Obtained from https://github.com/tseemann/snippy
[07:28:32] Detected operating system: linux
[07:28:32] Enabling bundled linux tools.
[07:28:32] Found bwa - /usr/local/bin/bwa
[07:28:32] Found bcftools - /usr/local/bin/bcftools
[07:28:32] Found samtools - /usr/local/bin/samtools
[07:28:32] Found java - /usr/local/bin/java
[07:28:32] Found snpEff - /usr/local/bin/snpEff
[07:28:32] Found samclip - /usr/local/bin/samclip
[07:28:32] Found seqtk - /usr/local/bin/seqtk
[07:28:32] Found parallel - /usr/local/bin/parallel
[07:28:32] Found freebayes - /usr/local/bin/freebayes
[07:28:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:28:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:28:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:28:32] Found vcfuniq - /usr/local/bin/vcfuniq
[07:28:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:28:32] Found gzip - /bin/gzip
[07:28:32] Found vt - /usr/local/bin/vt
[07:28:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:28:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:28:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:28:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:28:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:28:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:28:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:28:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:29:10] This is snippy 4.6.0Show full stderr[07:29:10] This is snippy 4.6.0
[07:29:10] Written by Torsten Seemann
[07:29:10] Obtained from https://github.com/tseemann/snippy
[07:29:10] Detected operating system: linux
[07:29:10] Enabling bundled linux tools.
[07:29:10] Found bwa - /usr/local/bin/bwa
[07:29:10] Found bcftools - /usr/local/bin/bcftools
[07:29:10] Found samtools - /usr/local/bin/samtools
[07:29:10] Found java - /usr/local/bin/java
[07:29:10] Found snpEff - /usr/local/bin/snpEff
[07:29:10] Found samclip - /usr/local/bin/samclip
[07:29:10] Found seqtk - /usr/local/bin/seqtk
[07:29:10] Found parallel - /usr/local/bin/parallel
[07:29:10] Found freebayes - /usr/local/bin/freebayes
[07:29:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:29:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:29:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:29:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:29:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:29:10] Found gzip - /bin/gzip
[07:29:10] Found vt - /usr/local/bin/vt
[07:29:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:29:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:29:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:29:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:29:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:29:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:29:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:29:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:29:46] This is snippy 4.6.0Show full stderr[07:29:46] This is snippy 4.6.0
[07:29:46] Written by Torsten Seemann
[07:29:46] Obtained from https://github.com/tseemann/snippy
[07:29:46] Detected operating system: linux
[07:29:46] Enabling bundled linux tools.
[07:29:46] Found bwa - /usr/local/bin/bwa
[07:29:46] Found bcftools - /usr/local/bin/bcftools
[07:29:46] Found samtools - /usr/local/bin/samtools
[07:29:46] Found java - /usr/local/bin/java
[07:29:46] Found snpEff - /usr/local/bin/snpEff
[07:29:46] Found samclip - /usr/local/bin/samclip
[07:29:46] Found seqtk - /usr/local/bin/seqtk
[07:29:46] Found parallel - /usr/local/bin/parallel
[07:29:46] Found freebayes - /usr/local/bin/freebayes
[07:29:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:29:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:29:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:29:46] Found vcfuniq - /usr/local/bin/vcfuniq
[07:29:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:29:46] Found gzip - /bin/gzip
[07:29:46] Found vt - /usr/local/bin/vt
[07:29:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:29:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:29:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:29:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:29:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:29:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:29:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:29:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:28:44] This is snippy 4.6.0Show full stderr[07:28:44] This is snippy 4.6.0
[07:28:44] Written by Torsten Seemann
[07:28:44] Obtained from https://github.com/tseemann/snippy
[07:28:44] Detected operating system: linux
[07:28:44] Enabling bundled linux tools.
[07:28:44] Found bwa - /usr/local/bin/bwa
[07:28:44] Found bcftools - /usr/local/bin/bcftools
[07:28:44] Found samtools - /usr/local/bin/samtools
[07:28:44] Found java - /usr/local/bin/java
[07:28:44] Found snpEff - /usr/local/bin/snpEff
[07:28:44] Found samclip - /usr/local/bin/samclip
[07:28:44] Found seqtk - /usr/local/bin/seqtk
[07:28:44] Found parallel - /usr/local/bin/parallel
[07:28:44] Found freebayes - /usr/local/bin/freebayes
[07:28:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:28:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:28:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:28:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:28:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:28:44] Found gzip - /bin/gzip
[07:28:44] Found vt - /usr/local/bin/vt
[07:28:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:28:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:28:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:28:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:28:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:28:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:28:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:28:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:31:34] This is snippy 4.6.0Show full stderr[07:31:34] This is snippy 4.6.0
[07:31:34] Written by Torsten Seemann
[07:31:34] Obtained from https://github.com/tseemann/snippy
[07:31:34] Detected operating system: linux
[07:31:34] Enabling bundled linux tools.
[07:31:34] Found bwa - /usr/local/bin/bwa
[07:31:34] Found bcftools - /usr/local/bin/bcftools
[07:31:34] Found samtools - /usr/local/bin/samtools
[07:31:34] Found java - /usr/local/bin/java
[07:31:34] Found snpEff - /usr/local/bin/snpEff
[07:31:34] Found samclip - /usr/local/bin/samclip
[07:31:34] Found seqtk - /usr/local/bin/seqtk
[07:31:34] Found parallel - /usr/local/bin/parallel
[07:31:34] Found freebayes - /usr/local/bin/freebayes
[07:31:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:31:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:31:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:31:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:31:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:31:34] Found gzip - /bin/gzip
[07:31:34] Found vt - /usr/local/bin/vt
[07:31:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:31:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:31:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:31:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:31:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:31:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:31:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:31:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:33:56] This is snippy 4.6.0Show full stderr[07:33:56] This is snippy 4.6.0
[07:33:56] Written by Torsten Seemann
[07:33:56] Obtained from https://github.com/tseemann/snippy
[07:33:56] Detected operating system: linux
[07:33:56] Enabling bundled linux tools.
[07:33:56] Found bwa - /usr/local/bin/bwa
[07:33:56] Found bcftools - /usr/local/bin/bcftools
[07:33:56] Found samtools - /usr/local/bin/samtools
[07:33:56] Found java - /usr/local/bin/java
[07:33:56] Found snpEff - /usr/local/bin/snpEff
[07:33:56] Found samclip - /usr/local/bin/samclip
[07:33:56] Found seqtk - /usr/local/bin/seqtk
[07:33:56] Found parallel - /usr/local/bin/parallel
[07:33:56] Found freebayes - /usr/local/bin/freebayes
[07:33:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:33:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:33:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:33:56] Found vcfuniq - /usr/local/bin/vcfuniq
[07:33:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:33:56] Found gzip - /bin/gzip
[07:33:56] Found vt - /usr/local/bin/vt
[07:33:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:33:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:33:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:33:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:33:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:33:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:33:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:33:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:33:59] This is snippy 4.6.0Show full stderr[07:33:59] This is snippy 4.6.0
[07:33:59] Written by Torsten Seemann
[07:33:59] Obtained from https://github.com/tseemann/snippy
[07:33:59] Detected operating system: linux
[07:33:59] Enabling bundled linux tools.
[07:33:59] Found bwa - /usr/local/bin/bwa
[07:33:59] Found bcftools - /usr/local/bin/bcftools
[07:33:59] Found samtools - /usr/local/bin/samtools
[07:33:59] Found java - /usr/local/bin/java
[07:33:59] Found snpEff - /usr/local/bin/snpEff
[07:33:59] Found samclip - /usr/local/bin/samclip
[07:33:59] Found seqtk - /usr/local/bin/seqtk
[07:33:59] Found parallel - /usr/local/bin/parallel
[07:33:59] Found freebayes - /usr/local/bin/freebayes
[07:33:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:33:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:33:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:33:59] Found vcfuniq - /usr/local/bin/vcfuniq
[07:33:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:33:59] Found gzip - /bin/gzip
[07:33:59] Found vt - /usr/local/bin/vt
[07:33:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:33:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:33:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:33:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:33:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:34:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:34:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:34:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:30:31] This is snippy 4.6.0Show full stderr[07:30:31] This is snippy 4.6.0
[07:30:31] Written by Torsten Seemann
[07:30:31] Obtained from https://github.com/tseemann/snippy
[07:30:31] Detected operating system: linux
[07:30:31] Enabling bundled linux tools.
[07:30:31] Found bwa - /usr/local/bin/bwa
[07:30:31] Found bcftools - /usr/local/bin/bcftools
[07:30:31] Found samtools - /usr/local/bin/samtools
[07:30:31] Found java - /usr/local/bin/java
[07:30:31] Found snpEff - /usr/local/bin/snpEff
[07:30:31] Found samclip - /usr/local/bin/samclip
[07:30:31] Found seqtk - /usr/local/bin/seqtk
[07:30:31] Found parallel - /usr/local/bin/parallel
[07:30:31] Found freebayes - /usr/local/bin/freebayes
[07:30:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:30:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:30:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:30:31] Found vcfuniq - /usr/local/bin/vcfuniq
[07:30:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:30:31] Found gzip - /bin/gzip
[07:30:31] Found vt - /usr/local/bin/vt
[07:30:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:30:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:30:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:30:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:30:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:30:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:30:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:30:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:34:37] This is snippy 4.6.0Show full stderr[07:34:37] This is snippy 4.6.0
[07:34:37] Written by Torsten Seemann
[07:34:37] Obtained from https://github.com/tseemann/snippy
[07:34:37] Detected operating system: linux
[07:34:37] Enabling bundled linux tools.
[07:34:37] Found bwa - /usr/local/bin/bwa
[07:34:37] Found bcftools - /usr/local/bin/bcftools
[07:34:37] Found samtools - /usr/local/bin/samtools
[07:34:37] Found java - /usr/local/bin/java
[07:34:37] Found snpEff - /usr/local/bin/snpEff
[07:34:37] Found samclip - /usr/local/bin/samclip
[07:34:37] Found seqtk - /usr/local/bin/seqtk
[07:34:37] Found parallel - /usr/local/bin/parallel
[07:34:37] Found freebayes - /usr/local/bin/freebayes
[07:34:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:34:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:34:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:34:37] Found vcfuniq - /usr/local/bin/vcfuniq
[07:34:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:34:37] Found gzip - /bin/gzip
[07:34:37] Found vt - /usr/local/bin/vt
[07:34:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:34:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:34:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:34:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:34:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:34:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:34:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:34:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:35:04] This is snippy 4.6.0Show full stderr[07:35:04] This is snippy 4.6.0
[07:35:04] Written by Torsten Seemann
[07:35:04] Obtained from https://github.com/tseemann/snippy
[07:35:04] Detected operating system: linux
[07:35:04] Enabling bundled linux tools.
[07:35:04] Found bwa - /usr/local/bin/bwa
[07:35:04] Found bcftools - /usr/local/bin/bcftools
[07:35:04] Found samtools - /usr/local/bin/samtools
[07:35:04] Found java - /usr/local/bin/java
[07:35:04] Found snpEff - /usr/local/bin/snpEff
[07:35:04] Found samclip - /usr/local/bin/samclip
[07:35:04] Found seqtk - /usr/local/bin/seqtk
[07:35:04] Found parallel - /usr/local/bin/parallel
[07:35:04] Found freebayes - /usr/local/bin/freebayes
[07:35:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:35:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:35:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:35:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:35:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:35:04] Found gzip - /bin/gzip
[07:35:04] Found vt - /usr/local/bin/vt
[07:35:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:35:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:35:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:35:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:35:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:35:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:35:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:35:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:35:33] This is snippy 4.6.0Show full stderr[07:35:33] This is snippy 4.6.0
[07:35:33] Written by Torsten Seemann
[07:35:33] Obtained from https://github.com/tseemann/snippy
[07:35:33] Detected operating system: linux
[07:35:33] Enabling bundled linux tools.
[07:35:33] Found bwa - /usr/local/bin/bwa
[07:35:33] Found bcftools - /usr/local/bin/bcftools
[07:35:33] Found samtools - /usr/local/bin/samtools
[07:35:33] Found java - /usr/local/bin/java
[07:35:33] Found snpEff - /usr/local/bin/snpEff
[07:35:33] Found samclip - /usr/local/bin/samclip
[07:35:33] Found seqtk - /usr/local/bin/seqtk
[07:35:33] Found parallel - /usr/local/bin/parallel
[07:35:33] Found freebayes - /usr/local/bin/freebayes
[07:35:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:35:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:35:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:35:33] Found vcfuniq - /usr/local/bin/vcfuniq
[07:35:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:35:33] Found gzip - /bin/gzip
[07:35:33] Found vt - /usr/local/bin/vt
[07:35:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:35:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:35:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:35:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:35:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:35:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:35:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:35:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:32:39] This is snippy 4.6.0Show full stderr[07:32:39] This is snippy 4.6.0
[07:32:39] Written by Torsten Seemann
[07:32:39] Obtained from https://github.com/tseemann/snippy
[07:32:39] Detected operating system: linux
[07:32:39] Enabling bundled linux tools.
[07:32:39] Found bwa - /usr/local/bin/bwa
[07:32:39] Found bcftools - /usr/local/bin/bcftools
[07:32:39] Found samtools - /usr/local/bin/samtools
[07:32:39] Found java - /usr/local/bin/java
[07:32:39] Found snpEff - /usr/local/bin/snpEff
[07:32:39] Found samclip - /usr/local/bin/samclip
[07:32:39] Found seqtk - /usr/local/bin/seqtk
[07:32:39] Found parallel - /usr/local/bin/parallel
[07:32:39] Found freebayes - /usr/local/bin/freebayes
[07:32:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:39] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:39] Found gzip - /bin/gzip
[07:32:39] Found vt - /usr/local/bin/vt
[07:32:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:32:51] This is snippy 4.6.0Show full stderr[07:32:51] This is snippy 4.6.0
[07:32:51] Written by Torsten Seemann
[07:32:51] Obtained from https://github.com/tseemann/snippy
[07:32:51] Detected operating system: linux
[07:32:51] Enabling bundled linux tools.
[07:32:51] Found bwa - /usr/local/bin/bwa
[07:32:51] Found bcftools - /usr/local/bin/bcftools
[07:32:51] Found samtools - /usr/local/bin/samtools
[07:32:51] Found java - /usr/local/bin/java
[07:32:51] Found snpEff - /usr/local/bin/snpEff
[07:32:51] Found samclip - /usr/local/bin/samclip
[07:32:51] Found seqtk - /usr/local/bin/seqtk
[07:32:51] Found parallel - /usr/local/bin/parallel
[07:32:51] Found freebayes - /usr/local/bin/freebayes
[07:32:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:51] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:51] Found gzip - /bin/gzip
[07:32:51] Found vt - /usr/local/bin/vt
[07:32:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:32:54] This is snippy 4.6.0Show full stderr[07:32:54] This is snippy 4.6.0
[07:32:54] Written by Torsten Seemann
[07:32:54] Obtained from https://github.com/tseemann/snippy
[07:32:54] Detected operating system: linux
[07:32:54] Enabling bundled linux tools.
[07:32:54] Found bwa - /usr/local/bin/bwa
[07:32:54] Found bcftools - /usr/local/bin/bcftools
[07:32:54] Found samtools - /usr/local/bin/samtools
[07:32:54] Found java - /usr/local/bin/java
[07:32:54] Found snpEff - /usr/local/bin/snpEff
[07:32:54] Found samclip - /usr/local/bin/samclip
[07:32:54] Found seqtk - /usr/local/bin/seqtk
[07:32:54] Found parallel - /usr/local/bin/parallel
[07:32:54] Found freebayes - /usr/local/bin/freebayes
[07:32:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:54] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:54] Found gzip - /bin/gzip
[07:32:54] Found vt - /usr/local/bin/vt
[07:32:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:35:19] This is snippy 4.6.0Show full stderr[07:35:19] This is snippy 4.6.0
[07:35:19] Written by Torsten Seemann
[07:35:19] Obtained from https://github.com/tseemann/snippy
[07:35:19] Detected operating system: linux
[07:35:19] Enabling bundled linux tools.
[07:35:19] Found bwa - /usr/local/bin/bwa
[07:35:19] Found bcftools - /usr/local/bin/bcftools
[07:35:19] Found samtools - /usr/local/bin/samtools
[07:35:19] Found java - /usr/local/bin/java
[07:35:19] Found snpEff - /usr/local/bin/snpEff
[07:35:19] Found samclip - /usr/local/bin/samclip
[07:35:19] Found seqtk - /usr/local/bin/seqtk
[07:35:19] Found parallel - /usr/local/bin/parallel
[07:35:19] Found freebayes - /usr/local/bin/freebayes
[07:35:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:35:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:35:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:35:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:35:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:35:19] Found gzip - /bin/gzip
[07:35:19] Found vt - /usr/local/bin/vt
[07:35:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:35:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:35:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:35:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:35:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:35:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:35:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:35:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:36:47] This is snippy 4.6.0Show full stderr[07:36:47] This is snippy 4.6.0
[07:36:47] Written by Torsten Seemann
[07:36:47] Obtained from https://github.com/tseemann/snippy
[07:36:47] Detected operating system: linux
[07:36:47] Enabling bundled linux tools.
[07:36:47] Found bwa - /usr/local/bin/bwa
[07:36:47] Found bcftools - /usr/local/bin/bcftools
[07:36:47] Found samtools - /usr/local/bin/samtools
[07:36:47] Found java - /usr/local/bin/java
[07:36:47] Found snpEff - /usr/local/bin/snpEff
[07:36:47] Found samclip - /usr/local/bin/samclip
[07:36:47] Found seqtk - /usr/local/bin/seqtk
[07:36:47] Found parallel - /usr/local/bin/parallel
[07:36:47] Found freebayes - /usr/local/bin/freebayes
[07:36:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:47] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:47] Found gzip - /bin/gzip
[07:36:47] Found vt - /usr/local/bin/vt
[07:36:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:37:02] This is snippy 4.6.0Show full stderr[07:37:02] This is snippy 4.6.0
[07:37:02] Written by Torsten Seemann
[07:37:02] Obtained from https://github.com/tseemann/snippy
[07:37:02] Detected operating system: linux
[07:37:02] Enabling bundled linux tools.
[07:37:02] Found bwa - /usr/local/bin/bwa
[07:37:02] Found bcftools - /usr/local/bin/bcftools
[07:37:02] Found samtools - /usr/local/bin/samtools
[07:37:02] Found java - /usr/local/bin/java
[07:37:02] Found snpEff - /usr/local/bin/snpEff
[07:37:02] Found samclip - /usr/local/bin/samclip
[07:37:02] Found seqtk - /usr/local/bin/seqtk
[07:37:02] Found parallel - /usr/local/bin/parallel
[07:37:02] Found freebayes - /usr/local/bin/freebayes
[07:37:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:37:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:37:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:37:02] Found vcfuniq - /usr/local/bin/vcfuniq
[07:37:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:37:02] Found gzip - /bin/gzip
[07:37:02] Found vt - /usr/local/bin/vt
[07:37:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:37:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:37:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:37:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:37:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:37:16] This is snippy 4.6.0Show full stderr[07:37:16] This is snippy 4.6.0
[07:37:16] Written by Torsten Seemann
[07:37:16] Obtained from https://github.com/tseemann/snippy
[07:37:16] Detected operating system: linux
[07:37:16] Enabling bundled linux tools.
[07:37:16] Found bwa - /usr/local/bin/bwa
[07:37:16] Found bcftools - /usr/local/bin/bcftools
[07:37:16] Found samtools - /usr/local/bin/samtools
[07:37:16] Found java - /usr/local/bin/java
[07:37:16] Found snpEff - /usr/local/bin/snpEff
[07:37:16] Found samclip - /usr/local/bin/samclip
[07:37:16] Found seqtk - /usr/local/bin/seqtk
[07:37:16] Found parallel - /usr/local/bin/parallel
[07:37:16] Found freebayes - /usr/local/bin/freebayes
[07:37:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:37:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:37:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:37:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:37:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:37:16] Found gzip - /bin/gzip
[07:37:16] Found vt - /usr/local/bin/vt
[07:37:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:37:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:37:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:37:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:37:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:37:28] This is snippy 4.6.0Show full stderr[07:37:28] This is snippy 4.6.0
[07:37:28] Written by Torsten Seemann
[07:37:28] Obtained from https://github.com/tseemann/snippy
[07:37:28] Detected operating system: linux
[07:37:28] Enabling bundled linux tools.
[07:37:28] Found bwa - /usr/local/bin/bwa
[07:37:28] Found bcftools - /usr/local/bin/bcftools
[07:37:28] Found samtools - /usr/local/bin/samtools
[07:37:28] Found java - /usr/local/bin/java
[07:37:28] Found snpEff - /usr/local/bin/snpEff
[07:37:28] Found samclip - /usr/local/bin/samclip
[07:37:28] Found seqtk - /usr/local/bin/seqtk
[07:37:28] Found parallel - /usr/local/bin/parallel
[07:37:28] Found freebayes - /usr/local/bin/freebayes
[07:37:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:37:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:37:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:37:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:37:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:37:28] Found gzip - /bin/gzip
[07:37:28] Found vt - /usr/local/bin/vt
[07:37:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:37:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:37:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:37:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:37:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:39:50] This is snippy 4.6.0Show full stderr[07:39:50] This is snippy 4.6.0
[07:39:50] Written by Torsten Seemann
[07:39:50] Obtained from https://github.com/tseemann/snippy
[07:39:50] Detected operating system: linux
[07:39:50] Enabling bundled linux tools.
[07:39:50] Found bwa - /usr/local/bin/bwa
[07:39:50] Found bcftools - /usr/local/bin/bcftools
[07:39:50] Found samtools - /usr/local/bin/samtools
[07:39:50] Found java - /usr/local/bin/java
[07:39:50] Found snpEff - /usr/local/bin/snpEff
[07:39:50] Found samclip - /usr/local/bin/samclip
[07:39:50] Found seqtk - /usr/local/bin/seqtk
[07:39:50] Found parallel - /usr/local/bin/parallel
[07:39:51] Found freebayes - /usr/local/bin/freebayes
[07:39:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:39:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:39:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:39:51] Found vcfuniq - /usr/local/bin/vcfuniq
[07:39:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:39:51] Found gzip - /bin/gzip
[07:39:51] Found vt - /usr/local/bin/vt
[07:39:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:39:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:39:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:39:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:39:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:39:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:39:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:39:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:33:04] This is snippy 4.6.0Show full stderr[07:33:04] This is snippy 4.6.0
[07:33:04] Written by Torsten Seemann
[07:33:04] Obtained from https://github.com/tseemann/snippy
[07:33:04] Detected operating system: linux
[07:33:04] Enabling bundled linux tools.
[07:33:04] Found bwa - /usr/local/bin/bwa
[07:33:04] Found bcftools - /usr/local/bin/bcftools
[07:33:04] Found samtools - /usr/local/bin/samtools
[07:33:04] Found java - /usr/local/bin/java
[07:33:04] Found snpEff - /usr/local/bin/snpEff
[07:33:04] Found samclip - /usr/local/bin/samclip
[07:33:04] Found seqtk - /usr/local/bin/seqtk
[07:33:04] Found parallel - /usr/local/bin/parallel
[07:33:04] Found freebayes - /usr/local/bin/freebayes
[07:33:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:33:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:33:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:33:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:33:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:33:04] Found gzip - /bin/gzip
[07:33:04] Found vt - /usr/local/bin/vt
[07:33:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:33:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:33:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:33:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:33:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:33:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:33:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:33:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:35:39] This is snippy 4.6.0Show full stderr[07:35:39] This is snippy 4.6.0
[07:35:39] Written by Torsten Seemann
[07:35:39] Obtained from https://github.com/tseemann/snippy
[07:35:39] Detected operating system: linux
[07:35:39] Enabling bundled linux tools.
[07:35:39] Found bwa - /usr/local/bin/bwa
[07:35:39] Found bcftools - /usr/local/bin/bcftools
[07:35:39] Found samtools - /usr/local/bin/samtools
[07:35:39] Found java - /usr/local/bin/java
[07:35:39] Found snpEff - /usr/local/bin/snpEff
[07:35:39] Found samclip - /usr/local/bin/samclip
[07:35:39] Found seqtk - /usr/local/bin/seqtk
[07:35:39] Found parallel - /usr/local/bin/parallel
[07:35:39] Found freebayes - /usr/local/bin/freebayes
[07:35:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:35:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:35:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:35:39] Found vcfuniq - /usr/local/bin/vcfuniq
[07:35:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:35:39] Found gzip - /bin/gzip
[07:35:39] Found vt - /usr/local/bin/vt
[07:35:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:35:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:35:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:35:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:35:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:35:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:35:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:35:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:36:34] This is snippy 4.6.0Show full stderr[07:36:34] This is snippy 4.6.0
[07:36:34] Written by Torsten Seemann
[07:36:34] Obtained from https://github.com/tseemann/snippy
[07:36:34] Detected operating system: linux
[07:36:34] Enabling bundled linux tools.
[07:36:34] Found bwa - /usr/local/bin/bwa
[07:36:34] Found bcftools - /usr/local/bin/bcftools
[07:36:34] Found samtools - /usr/local/bin/samtools
[07:36:34] Found java - /usr/local/bin/java
[07:36:34] Found snpEff - /usr/local/bin/snpEff
[07:36:34] Found samclip - /usr/local/bin/samclip
[07:36:34] Found seqtk - /usr/local/bin/seqtk
[07:36:34] Found parallel - /usr/local/bin/parallel
[07:36:34] Found freebayes - /usr/local/bin/freebayes
[07:36:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:34] Found gzip - /bin/gzip
[07:36:34] Found vt - /usr/local/bin/vt
[07:36:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:38:25] This is snippy 4.6.0Show full stderr[07:38:25] This is snippy 4.6.0
[07:38:25] Written by Torsten Seemann
[07:38:25] Obtained from https://github.com/tseemann/snippy
[07:38:25] Detected operating system: linux
[07:38:25] Enabling bundled linux tools.
[07:38:25] Found bwa - /usr/local/bin/bwa
[07:38:25] Found bcftools - /usr/local/bin/bcftools
[07:38:25] Found samtools - /usr/local/bin/samtools
[07:38:25] Found java - /usr/local/bin/java
[07:38:25] Found snpEff - /usr/local/bin/snpEff
[07:38:25] Found samclip - /usr/local/bin/samclip
[07:38:25] Found seqtk - /usr/local/bin/seqtk
[07:38:25] Found parallel - /usr/local/bin/parallel
[07:38:25] Found freebayes - /usr/local/bin/freebayes
[07:38:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:25] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:25] Found gzip - /bin/gzip
[07:38:25] Found vt - /usr/local/bin/vt
[07:38:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:40:21] This is snippy 4.6.0Show full stderr[07:40:21] This is snippy 4.6.0
[07:40:21] Written by Torsten Seemann
[07:40:21] Obtained from https://github.com/tseemann/snippy
[07:40:21] Detected operating system: linux
[07:40:21] Enabling bundled linux tools.
[07:40:21] Found bwa - /usr/local/bin/bwa
[07:40:21] Found bcftools - /usr/local/bin/bcftools
[07:40:21] Found samtools - /usr/local/bin/samtools
[07:40:21] Found java - /usr/local/bin/java
[07:40:21] Found snpEff - /usr/local/bin/snpEff
[07:40:22] Found samclip - /usr/local/bin/samclip
[07:40:22] Found seqtk - /usr/local/bin/seqtk
[07:40:22] Found parallel - /usr/local/bin/parallel
[07:40:22] Found freebayes - /usr/local/bin/freebayes
[07:40:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:22] Found gzip - /bin/gzip
[07:40:22] Found vt - /usr/local/bin/vt
[07:40:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:40:51] This is snippy 4.6.0Show full stderr[07:40:51] This is snippy 4.6.0
[07:40:51] Written by Torsten Seemann
[07:40:51] Obtained from https://github.com/tseemann/snippy
[07:40:51] Detected operating system: linux
[07:40:51] Enabling bundled linux tools.
[07:40:51] Found bwa - /usr/local/bin/bwa
[07:40:51] Found bcftools - /usr/local/bin/bcftools
[07:40:51] Found samtools - /usr/local/bin/samtools
[07:40:51] Found java - /usr/local/bin/java
[07:40:51] Found snpEff - /usr/local/bin/snpEff
[07:40:51] Found samclip - /usr/local/bin/samclip
[07:40:51] Found seqtk - /usr/local/bin/seqtk
[07:40:51] Found parallel - /usr/local/bin/parallel
[07:40:51] Found freebayes - /usr/local/bin/freebayes
[07:40:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:51] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:51] Found gzip - /bin/gzip
[07:40:51] Found vt - /usr/local/bin/vt
[07:40:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:41:19] This is snippy 4.6.0Show full stderr[07:41:19] This is snippy 4.6.0
[07:41:19] Written by Torsten Seemann
[07:41:19] Obtained from https://github.com/tseemann/snippy
[07:41:19] Detected operating system: linux
[07:41:19] Enabling bundled linux tools.
[07:41:19] Found bwa - /usr/local/bin/bwa
[07:41:19] Found bcftools - /usr/local/bin/bcftools
[07:41:19] Found samtools - /usr/local/bin/samtools
[07:41:19] Found java - /usr/local/bin/java
[07:41:19] Found snpEff - /usr/local/bin/snpEff
[07:41:19] Found samclip - /usr/local/bin/samclip
[07:41:19] Found seqtk - /usr/local/bin/seqtk
[07:41:19] Found parallel - /usr/local/bin/parallel
[07:41:19] Found freebayes - /usr/local/bin/freebayes
[07:41:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:41:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:41:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:41:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:41:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:41:19] Found gzip - /bin/gzip
[07:41:19] Found vt - /usr/local/bin/vt
[07:41:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:41:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:41:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:41:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:41:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:41:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:41:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:41:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:41:28] This is snippy 4.6.0Show full stderr[07:41:28] This is snippy 4.6.0
[07:41:28] Written by Torsten Seemann
[07:41:28] Obtained from https://github.com/tseemann/snippy
[07:41:28] Detected operating system: linux
[07:41:28] Enabling bundled linux tools.
[07:41:28] Found bwa - /usr/local/bin/bwa
[07:41:28] Found bcftools - /usr/local/bin/bcftools
[07:41:28] Found samtools - /usr/local/bin/samtools
[07:41:28] Found java - /usr/local/bin/java
[07:41:28] Found snpEff - /usr/local/bin/snpEff
[07:41:28] Found samclip - /usr/local/bin/samclip
[07:41:28] Found seqtk - /usr/local/bin/seqtk
[07:41:28] Found parallel - /usr/local/bin/parallel
[07:41:28] Found freebayes - /usr/local/bin/freebayes
[07:41:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:41:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:41:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:41:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:41:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:41:28] Found gzip - /bin/gzip
[07:41:28] Found vt - /usr/local/bin/vt
[07:41:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:41:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:41:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:41:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:41:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:41:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:41:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:41:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:40:04] This is snippy 4.6.0Show full stderr[07:40:04] This is snippy 4.6.0
[07:40:04] Written by Torsten Seemann
[07:40:04] Obtained from https://github.com/tseemann/snippy
[07:40:04] Detected operating system: linux
[07:40:04] Enabling bundled linux tools.
[07:40:04] Found bwa - /usr/local/bin/bwa
[07:40:04] Found bcftools - /usr/local/bin/bcftools
[07:40:04] Found samtools - /usr/local/bin/samtools
[07:40:04] Found java - /usr/local/bin/java
[07:40:04] Found snpEff - /usr/local/bin/snpEff
[07:40:04] Found samclip - /usr/local/bin/samclip
[07:40:04] Found seqtk - /usr/local/bin/seqtk
[07:40:04] Found parallel - /usr/local/bin/parallel
[07:40:04] Found freebayes - /usr/local/bin/freebayes
[07:40:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:04] Found gzip - /bin/gzip
[07:40:04] Found vt - /usr/local/bin/vt
[07:40:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:41:49] This is snippy 4.6.0Show full stderr[07:41:49] This is snippy 4.6.0
[07:41:49] Written by Torsten Seemann
[07:41:49] Obtained from https://github.com/tseemann/snippy
[07:41:49] Detected operating system: linux
[07:41:49] Enabling bundled linux tools.
[07:41:49] Found bwa - /usr/local/bin/bwa
[07:41:49] Found bcftools - /usr/local/bin/bcftools
[07:41:49] Found samtools - /usr/local/bin/samtools
[07:41:49] Found java - /usr/local/bin/java
[07:41:49] Found snpEff - /usr/local/bin/snpEff
[07:41:49] Found samclip - /usr/local/bin/samclip
[07:41:49] Found seqtk - /usr/local/bin/seqtk
[07:41:49] Found parallel - /usr/local/bin/parallel
[07:41:49] Found freebayes - /usr/local/bin/freebayes
[07:41:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:41:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:41:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:41:49] Found vcfuniq - /usr/local/bin/vcfuniq
[07:41:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:41:49] Found gzip - /bin/gzip
[07:41:49] Found vt - /usr/local/bin/vt
[07:41:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:41:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:41:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:41:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:41:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:41:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:41:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:41:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:38:39] This is snippy 4.6.0Show full stderr[07:38:39] This is snippy 4.6.0
[07:38:39] Written by Torsten Seemann
[07:38:39] Obtained from https://github.com/tseemann/snippy
[07:38:39] Detected operating system: linux
[07:38:39] Enabling bundled linux tools.
[07:38:39] Found bwa - /usr/local/bin/bwa
[07:38:39] Found bcftools - /usr/local/bin/bcftools
[07:38:39] Found samtools - /usr/local/bin/samtools
[07:38:39] Found java - /usr/local/bin/java
[07:38:39] Found snpEff - /usr/local/bin/snpEff
[07:38:39] Found samclip - /usr/local/bin/samclip
[07:38:39] Found seqtk - /usr/local/bin/seqtk
[07:38:39] Found parallel - /usr/local/bin/parallel
[07:38:39] Found freebayes - /usr/local/bin/freebayes
[07:38:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:39] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:39] Found gzip - /bin/gzip
[07:38:39] Found vt - /usr/local/bin/vt
[07:38:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:39:06] This is snippy 4.6.0Show full stderr[07:39:06] This is snippy 4.6.0
[07:39:06] Written by Torsten Seemann
[07:39:06] Obtained from https://github.com/tseemann/snippy
[07:39:06] Detected operating system: linux
[07:39:06] Enabling bundled linux tools.
[07:39:06] Found bwa - /usr/local/bin/bwa
[07:39:06] Found bcftools - /usr/local/bin/bcftools
[07:39:06] Found samtools - /usr/local/bin/samtools
[07:39:06] Found java - /usr/local/bin/java
[07:39:06] Found snpEff - /usr/local/bin/snpEff
[07:39:06] Found samclip - /usr/local/bin/samclip
[07:39:06] Found seqtk - /usr/local/bin/seqtk
[07:39:06] Found parallel - /usr/local/bin/parallel
[07:39:06] Found freebayes - /usr/local/bin/freebayes
[07:39:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:39:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:39:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:39:06] Found vcfuniq - /usr/local/bin/vcfuniq
[07:39:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:39:07] Found gzip - /bin/gzip
[07:39:07] Found vt - /usr/local/bin/vt
[07:39:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:39:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:39:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:39:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:39:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:39:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:39:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:39:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:39:21] This is snippy 4.6.0Show full stderr[07:39:21] This is snippy 4.6.0
[07:39:21] Written by Torsten Seemann
[07:39:21] Obtained from https://github.com/tseemann/snippy
[07:39:21] Detected operating system: linux
[07:39:21] Enabling bundled linux tools.
[07:39:21] Found bwa - /usr/local/bin/bwa
[07:39:21] Found bcftools - /usr/local/bin/bcftools
[07:39:21] Found samtools - /usr/local/bin/samtools
[07:39:21] Found java - /usr/local/bin/java
[07:39:21] Found snpEff - /usr/local/bin/snpEff
[07:39:21] Found samclip - /usr/local/bin/samclip
[07:39:21] Found seqtk - /usr/local/bin/seqtk
[07:39:21] Found parallel - /usr/local/bin/parallel
[07:39:21] Found freebayes - /usr/local/bin/freebayes
[07:39:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:39:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:39:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:39:21] Found vcfuniq - /usr/local/bin/vcfuniq
[07:39:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:39:22] Found gzip - /bin/gzip
[07:39:22] Found vt - /usr/local/bin/vt
[07:39:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:39:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:39:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:39:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:39:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:39:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:39:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:39:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:39:24] This is snippy 4.6.0Show full stderr[07:39:24] This is snippy 4.6.0
[07:39:24] Written by Torsten Seemann
[07:39:24] Obtained from https://github.com/tseemann/snippy
[07:39:24] Detected operating system: linux
[07:39:24] Enabling bundled linux tools.
[07:39:24] Found bwa - /usr/local/bin/bwa
[07:39:24] Found bcftools - /usr/local/bin/bcftools
[07:39:24] Found samtools - /usr/local/bin/samtools
[07:39:24] Found java - /usr/local/bin/java
[07:39:24] Found snpEff - /usr/local/bin/snpEff
[07:39:24] Found samclip - /usr/local/bin/samclip
[07:39:24] Found seqtk - /usr/local/bin/seqtk
[07:39:24] Found parallel - /usr/local/bin/parallel
[07:39:24] Found freebayes - /usr/local/bin/freebayes
[07:39:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:39:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:39:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:39:24] Found vcfuniq - /usr/local/bin/vcfuniq
[07:39:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:39:24] Found gzip - /bin/gzip
[07:39:24] Found vt - /usr/local/bin/vt
[07:39:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:39:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:39:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:39:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:39:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:39:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:39:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:39:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:42:02] This is snippy 4.6.0Show full stderr[07:42:02] This is snippy 4.6.0
[07:42:02] Written by Torsten Seemann
[07:42:02] Obtained from https://github.com/tseemann/snippy
[07:42:02] Detected operating system: linux
[07:42:02] Enabling bundled linux tools.
[07:42:02] Found bwa - /usr/local/bin/bwa
[07:42:02] Found bcftools - /usr/local/bin/bcftools
[07:42:02] Found samtools - /usr/local/bin/samtools
[07:42:02] Found java - /usr/local/bin/java
[07:42:02] Found snpEff - /usr/local/bin/snpEff
[07:42:02] Found samclip - /usr/local/bin/samclip
[07:42:02] Found seqtk - /usr/local/bin/seqtk
[07:42:02] Found parallel - /usr/local/bin/parallel
[07:42:02] Found freebayes - /usr/local/bin/freebayes
[07:42:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:02] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:02] Found gzip - /bin/gzip
[07:42:02] Found vt - /usr/local/bin/vt
[07:42:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:44:43] This is snippy 4.6.0Show full stderr[07:44:43] This is snippy 4.6.0
[07:44:43] Written by Torsten Seemann
[07:44:43] Obtained from https://github.com/tseemann/snippy
[07:44:43] Detected operating system: linux
[07:44:43] Enabling bundled linux tools.
[07:44:43] Found bwa - /usr/local/bin/bwa
[07:44:43] Found bcftools - /usr/local/bin/bcftools
[07:44:43] Found samtools - /usr/local/bin/samtools
[07:44:43] Found java - /usr/local/bin/java
[07:44:43] Found snpEff - /usr/local/bin/snpEff
[07:44:43] Found samclip - /usr/local/bin/samclip
[07:44:43] Found seqtk - /usr/local/bin/seqtk
[07:44:43] Found parallel - /usr/local/bin/parallel
[07:44:43] Found freebayes - /usr/local/bin/freebayes
[07:44:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:43] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:43] Found gzip - /bin/gzip
[07:44:43] Found vt - /usr/local/bin/vt
[07:44:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:46:16] This is snippy 4.6.0Show full stderr[07:46:16] This is snippy 4.6.0
[07:46:16] Written by Torsten Seemann
[07:46:16] Obtained from https://github.com/tseemann/snippy
[07:46:16] Detected operating system: linux
[07:46:16] Enabling bundled linux tools.
[07:46:16] Found bwa - /usr/local/bin/bwa
[07:46:16] Found bcftools - /usr/local/bin/bcftools
[07:46:16] Found samtools - /usr/local/bin/samtools
[07:46:16] Found java - /usr/local/bin/java
[07:46:16] Found snpEff - /usr/local/bin/snpEff
[07:46:16] Found samclip - /usr/local/bin/samclip
[07:46:16] Found seqtk - /usr/local/bin/seqtk
[07:46:16] Found parallel - /usr/local/bin/parallel
[07:46:16] Found freebayes - /usr/local/bin/freebayes
[07:46:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:16] Found gzip - /bin/gzip
[07:46:16] Found vt - /usr/local/bin/vt
[07:46:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:46:43] This is snippy 4.6.0Show full stderr[07:46:43] This is snippy 4.6.0
[07:46:43] Written by Torsten Seemann
[07:46:43] Obtained from https://github.com/tseemann/snippy
[07:46:43] Detected operating system: linux
[07:46:43] Enabling bundled linux tools.
[07:46:43] Found bwa - /usr/local/bin/bwa
[07:46:43] Found bcftools - /usr/local/bin/bcftools
[07:46:43] Found samtools - /usr/local/bin/samtools
[07:46:43] Found java - /usr/local/bin/java
[07:46:43] Found snpEff - /usr/local/bin/snpEff
[07:46:43] Found samclip - /usr/local/bin/samclip
[07:46:43] Found seqtk - /usr/local/bin/seqtk
[07:46:43] Found parallel - /usr/local/bin/parallel
[07:46:43] Found freebayes - /usr/local/bin/freebayes
[07:46:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:43] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:43] Found gzip - /bin/gzip
[07:46:43] Found vt - /usr/local/bin/vt
[07:46:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:46:58] This is snippy 4.6.0Show full stderr[07:46:58] This is snippy 4.6.0
[07:46:58] Written by Torsten Seemann
[07:46:58] Obtained from https://github.com/tseemann/snippy
[07:46:58] Detected operating system: linux
[07:46:58] Enabling bundled linux tools.
[07:46:58] Found bwa - /usr/local/bin/bwa
[07:46:58] Found bcftools - /usr/local/bin/bcftools
[07:46:58] Found samtools - /usr/local/bin/samtools
[07:46:58] Found java - /usr/local/bin/java
[07:46:58] Found snpEff - /usr/local/bin/snpEff
[07:46:58] Found samclip - /usr/local/bin/samclip
[07:46:58] Found seqtk - /usr/local/bin/seqtk
[07:46:58] Found parallel - /usr/local/bin/parallel
[07:46:58] Found freebayes - /usr/local/bin/freebayes
[07:46:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:58] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:58] Found gzip - /bin/gzip
[07:46:58] Found vt - /usr/local/bin/vt
[07:46:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:43:22] This is snippy 4.6.0Show full stderr[07:43:22] This is snippy 4.6.0
[07:43:22] Written by Torsten Seemann
[07:43:22] Obtained from https://github.com/tseemann/snippy
[07:43:22] Detected operating system: linux
[07:43:22] Enabling bundled linux tools.
[07:43:22] Found bwa - /usr/local/bin/bwa
[07:43:22] Found bcftools - /usr/local/bin/bcftools
[07:43:22] Found samtools - /usr/local/bin/samtools
[07:43:22] Found java - /usr/local/bin/java
[07:43:22] Found snpEff - /usr/local/bin/snpEff
[07:43:22] Found samclip - /usr/local/bin/samclip
[07:43:22] Found seqtk - /usr/local/bin/seqtk
[07:43:22] Found parallel - /usr/local/bin/parallel
[07:43:22] Found freebayes - /usr/local/bin/freebayes
[07:43:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:22] Found gzip - /bin/gzip
[07:43:22] Found vt - /usr/local/bin/vt
[07:43:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:46:31] This is snippy 4.6.0Show full stderr[07:46:31] This is snippy 4.6.0
[07:46:31] Written by Torsten Seemann
[07:46:31] Obtained from https://github.com/tseemann/snippy
[07:46:31] Detected operating system: linux
[07:46:31] Enabling bundled linux tools.
[07:46:31] Found bwa - /usr/local/bin/bwa
[07:46:31] Found bcftools - /usr/local/bin/bcftools
[07:46:31] Found samtools - /usr/local/bin/samtools
[07:46:31] Found java - /usr/local/bin/java
[07:46:31] Found snpEff - /usr/local/bin/snpEff
[07:46:31] Found samclip - /usr/local/bin/samclip
[07:46:31] Found seqtk - /usr/local/bin/seqtk
[07:46:31] Found parallel - /usr/local/bin/parallel
[07:46:31] Found freebayes - /usr/local/bin/freebayes
[07:46:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:31] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:31] Found gzip - /bin/gzip
[07:46:31] Found vt - /usr/local/bin/vt
[07:46:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:39:36] This is snippy 4.6.0Show full stderr[07:39:36] This is snippy 4.6.0
[07:39:36] Written by Torsten Seemann
[07:39:36] Obtained from https://github.com/tseemann/snippy
[07:39:36] Detected operating system: linux
[07:39:36] Enabling bundled linux tools.
[07:39:36] Found bwa - /usr/local/bin/bwa
[07:39:36] Found bcftools - /usr/local/bin/bcftools
[07:39:36] Found samtools - /usr/local/bin/samtools
[07:39:36] Found java - /usr/local/bin/java
[07:39:36] Found snpEff - /usr/local/bin/snpEff
[07:39:36] Found samclip - /usr/local/bin/samclip
[07:39:36] Found seqtk - /usr/local/bin/seqtk
[07:39:36] Found parallel - /usr/local/bin/parallel
[07:39:36] Found freebayes - /usr/local/bin/freebayes
[07:39:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:39:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:39:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:39:36] Found vcfuniq - /usr/local/bin/vcfuniq
[07:39:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:39:36] Found gzip - /bin/gzip
[07:39:36] Found vt - /usr/local/bin/vt
[07:39:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:39:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:39:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:39:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:39:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:39:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:39:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:39:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:41:34] This is snippy 4.6.0Show full stderr[07:41:34] This is snippy 4.6.0
[07:41:34] Written by Torsten Seemann
[07:41:34] Obtained from https://github.com/tseemann/snippy
[07:41:34] Detected operating system: linux
[07:41:34] Enabling bundled linux tools.
[07:41:34] Found bwa - /usr/local/bin/bwa
[07:41:34] Found bcftools - /usr/local/bin/bcftools
[07:41:34] Found samtools - /usr/local/bin/samtools
[07:41:34] Found java - /usr/local/bin/java
[07:41:34] Found snpEff - /usr/local/bin/snpEff
[07:41:34] Found samclip - /usr/local/bin/samclip
[07:41:34] Found seqtk - /usr/local/bin/seqtk
[07:41:34] Found parallel - /usr/local/bin/parallel
[07:41:34] Found freebayes - /usr/local/bin/freebayes
[07:41:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:41:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:41:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:41:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:41:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:41:34] Found gzip - /bin/gzip
[07:41:34] Found vt - /usr/local/bin/vt
[07:41:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:41:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:41:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:41:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:41:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:41:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:41:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:41:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:41:56] This is snippy 4.6.0Show full stderr[07:41:56] This is snippy 4.6.0
[07:41:56] Written by Torsten Seemann
[07:41:56] Obtained from https://github.com/tseemann/snippy
[07:41:56] Detected operating system: linux
[07:41:56] Enabling bundled linux tools.
[07:41:56] Found bwa - /usr/local/bin/bwa
[07:41:56] Found bcftools - /usr/local/bin/bcftools
[07:41:56] Found samtools - /usr/local/bin/samtools
[07:41:56] Found java - /usr/local/bin/java
[07:41:56] Found snpEff - /usr/local/bin/snpEff
[07:41:56] Found samclip - /usr/local/bin/samclip
[07:41:56] Found seqtk - /usr/local/bin/seqtk
[07:41:56] Found parallel - /usr/local/bin/parallel
[07:41:56] Found freebayes - /usr/local/bin/freebayes
[07:41:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:41:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:41:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:41:56] Found vcfuniq - /usr/local/bin/vcfuniq
[07:41:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:41:56] Found gzip - /bin/gzip
[07:41:56] Found vt - /usr/local/bin/vt
[07:41:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:41:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:41:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:41:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:41:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:41:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:41:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:41:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:42:16] This is snippy 4.6.0Show full stderr[07:42:16] This is snippy 4.6.0
[07:42:16] Written by Torsten Seemann
[07:42:16] Obtained from https://github.com/tseemann/snippy
[07:42:16] Detected operating system: linux
[07:42:16] Enabling bundled linux tools.
[07:42:16] Found bwa - /usr/local/bin/bwa
[07:42:16] Found bcftools - /usr/local/bin/bcftools
[07:42:16] Found samtools - /usr/local/bin/samtools
[07:42:16] Found java - /usr/local/bin/java
[07:42:16] Found snpEff - /usr/local/bin/snpEff
[07:42:16] Found samclip - /usr/local/bin/samclip
[07:42:16] Found seqtk - /usr/local/bin/seqtk
[07:42:16] Found parallel - /usr/local/bin/parallel
[07:42:16] Found freebayes - /usr/local/bin/freebayes
[07:42:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:16] Found gzip - /bin/gzip
[07:42:16] Found vt - /usr/local/bin/vt
[07:42:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:47:41] This is snippy 4.6.0Show full stderr[07:47:41] This is snippy 4.6.0
[07:47:41] Written by Torsten Seemann
[07:47:41] Obtained from https://github.com/tseemann/snippy
[07:47:41] Detected operating system: linux
[07:47:41] Enabling bundled linux tools.
[07:47:41] Found bwa - /usr/local/bin/bwa
[07:47:41] Found bcftools - /usr/local/bin/bcftools
[07:47:41] Found samtools - /usr/local/bin/samtools
[07:47:41] Found java - /usr/local/bin/java
[07:47:41] Found snpEff - /usr/local/bin/snpEff
[07:47:41] Found samclip - /usr/local/bin/samclip
[07:47:41] Found seqtk - /usr/local/bin/seqtk
[07:47:41] Found parallel - /usr/local/bin/parallel
[07:47:41] Found freebayes - /usr/local/bin/freebayes
[07:47:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:47:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:47:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:47:41] Found vcfuniq - /usr/local/bin/vcfuniq
[07:47:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:47:41] Found gzip - /bin/gzip
[07:47:41] Found vt - /usr/local/bin/vt
[07:47:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:47:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:47:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:47:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:47:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:47:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:47:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:47:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:47:53] This is snippy 4.6.0Show full stderr[07:47:53] This is snippy 4.6.0
[07:47:53] Written by Torsten Seemann
[07:47:53] Obtained from https://github.com/tseemann/snippy
[07:47:53] Detected operating system: linux
[07:47:53] Enabling bundled linux tools.
[07:47:53] Found bwa - /usr/local/bin/bwa
[07:47:53] Found bcftools - /usr/local/bin/bcftools
[07:47:53] Found samtools - /usr/local/bin/samtools
[07:47:53] Found java - /usr/local/bin/java
[07:47:53] Found snpEff - /usr/local/bin/snpEff
[07:47:53] Found samclip - /usr/local/bin/samclip
[07:47:53] Found seqtk - /usr/local/bin/seqtk
[07:47:53] Found parallel - /usr/local/bin/parallel
[07:47:53] Found freebayes - /usr/local/bin/freebayes
[07:47:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:47:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:47:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:47:53] Found vcfuniq - /usr/local/bin/vcfuniq
[07:47:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:47:53] Found gzip - /bin/gzip
[07:47:53] Found vt - /usr/local/bin/vt
[07:47:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:47:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:47:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:47:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:47:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:47:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:47:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:47:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:48:07] This is snippy 4.6.0Show full stderr[07:48:07] This is snippy 4.6.0
[07:48:07] Written by Torsten Seemann
[07:48:07] Obtained from https://github.com/tseemann/snippy
[07:48:07] Detected operating system: linux
[07:48:07] Enabling bundled linux tools.
[07:48:07] Found bwa - /usr/local/bin/bwa
[07:48:07] Found bcftools - /usr/local/bin/bcftools
[07:48:07] Found samtools - /usr/local/bin/samtools
[07:48:07] Found java - /usr/local/bin/java
[07:48:07] Found snpEff - /usr/local/bin/snpEff
[07:48:07] Found samclip - /usr/local/bin/samclip
[07:48:07] Found seqtk - /usr/local/bin/seqtk
[07:48:07] Found parallel - /usr/local/bin/parallel
[07:48:07] Found freebayes - /usr/local/bin/freebayes
[07:48:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:07] Found gzip - /bin/gzip
[07:48:07] Found vt - /usr/local/bin/vt
[07:48:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:48:47] This is snippy 4.6.0Show full stderr[07:48:47] This is snippy 4.6.0
[07:48:47] Written by Torsten Seemann
[07:48:47] Obtained from https://github.com/tseemann/snippy
[07:48:47] Detected operating system: linux
[07:48:47] Enabling bundled linux tools.
[07:48:47] Found bwa - /usr/local/bin/bwa
[07:48:47] Found bcftools - /usr/local/bin/bcftools
[07:48:47] Found samtools - /usr/local/bin/samtools
[07:48:47] Found java - /usr/local/bin/java
[07:48:47] Found snpEff - /usr/local/bin/snpEff
[07:48:47] Found samclip - /usr/local/bin/samclip
[07:48:47] Found seqtk - /usr/local/bin/seqtk
[07:48:47] Found parallel - /usr/local/bin/parallel
[07:48:47] Found freebayes - /usr/local/bin/freebayes
[07:48:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:47] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:47] Found gzip - /bin/gzip
[07:48:47] Found vt - /usr/local/bin/vt
[07:48:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:43:10] This is snippy 4.6.0Show full stderr[07:43:10] This is snippy 4.6.0
[07:43:10] Written by Torsten Seemann
[07:43:10] Obtained from https://github.com/tseemann/snippy
[07:43:10] Detected operating system: linux
[07:43:10] Enabling bundled linux tools.
[07:43:10] Found bwa - /usr/local/bin/bwa
[07:43:10] Found bcftools - /usr/local/bin/bcftools
[07:43:10] Found samtools - /usr/local/bin/samtools
[07:43:10] Found java - /usr/local/bin/java
[07:43:10] Found snpEff - /usr/local/bin/snpEff
[07:43:10] Found samclip - /usr/local/bin/samclip
[07:43:10] Found seqtk - /usr/local/bin/seqtk
[07:43:10] Found parallel - /usr/local/bin/parallel
[07:43:10] Found freebayes - /usr/local/bin/freebayes
[07:43:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:10] Found gzip - /bin/gzip
[07:43:10] Found vt - /usr/local/bin/vt
[07:43:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:43:48] This is snippy 4.6.0Show full stderr[07:43:48] This is snippy 4.6.0
[07:43:48] Written by Torsten Seemann
[07:43:48] Obtained from https://github.com/tseemann/snippy
[07:43:48] Detected operating system: linux
[07:43:48] Enabling bundled linux tools.
[07:43:48] Found bwa - /usr/local/bin/bwa
[07:43:48] Found bcftools - /usr/local/bin/bcftools
[07:43:48] Found samtools - /usr/local/bin/samtools
[07:43:48] Found java - /usr/local/bin/java
[07:43:48] Found snpEff - /usr/local/bin/snpEff
[07:43:48] Found samclip - /usr/local/bin/samclip
[07:43:48] Found seqtk - /usr/local/bin/seqtk
[07:43:48] Found parallel - /usr/local/bin/parallel
[07:43:48] Found freebayes - /usr/local/bin/freebayes
[07:43:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:48] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:48] Found gzip - /bin/gzip
[07:43:48] Found vt - /usr/local/bin/vt
[07:43:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:44:28] This is snippy 4.6.0Show full stderr[07:44:28] This is snippy 4.6.0
[07:44:28] Written by Torsten Seemann
[07:44:28] Obtained from https://github.com/tseemann/snippy
[07:44:28] Detected operating system: linux
[07:44:28] Enabling bundled linux tools.
[07:44:28] Found bwa - /usr/local/bin/bwa
[07:44:28] Found bcftools - /usr/local/bin/bcftools
[07:44:28] Found samtools - /usr/local/bin/samtools
[07:44:28] Found java - /usr/local/bin/java
[07:44:28] Found snpEff - /usr/local/bin/snpEff
[07:44:28] Found samclip - /usr/local/bin/samclip
[07:44:28] Found seqtk - /usr/local/bin/seqtk
[07:44:28] Found parallel - /usr/local/bin/parallel
[07:44:28] Found freebayes - /usr/local/bin/freebayes
[07:44:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:28] Found gzip - /bin/gzip
[07:44:28] Found vt - /usr/local/bin/vt
[07:44:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:42:40] This is snippy 4.6.0Show full stderr[07:42:40] This is snippy 4.6.0
[07:42:40] Written by Torsten Seemann
[07:42:40] Obtained from https://github.com/tseemann/snippy
[07:42:40] Detected operating system: linux
[07:42:40] Enabling bundled linux tools.
[07:42:40] Found bwa - /usr/local/bin/bwa
[07:42:40] Found bcftools - /usr/local/bin/bcftools
[07:42:40] Found samtools - /usr/local/bin/samtools
[07:42:40] Found java - /usr/local/bin/java
[07:42:40] Found snpEff - /usr/local/bin/snpEff
[07:42:40] Found samclip - /usr/local/bin/samclip
[07:42:40] Found seqtk - /usr/local/bin/seqtk
[07:42:40] Found parallel - /usr/local/bin/parallel
[07:42:40] Found freebayes - /usr/local/bin/freebayes
[07:42:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:40] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:40] Found gzip - /bin/gzip
[07:42:40] Found vt - /usr/local/bin/vt
[07:42:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:42:55] This is snippy 4.6.0Show full stderr[07:42:55] This is snippy 4.6.0
[07:42:55] Written by Torsten Seemann
[07:42:55] Obtained from https://github.com/tseemann/snippy
[07:42:55] Detected operating system: linux
[07:42:55] Enabling bundled linux tools.
[07:42:55] Found bwa - /usr/local/bin/bwa
[07:42:55] Found bcftools - /usr/local/bin/bcftools
[07:42:55] Found samtools - /usr/local/bin/samtools
[07:42:55] Found java - /usr/local/bin/java
[07:42:55] Found snpEff - /usr/local/bin/snpEff
[07:42:55] Found samclip - /usr/local/bin/samclip
[07:42:55] Found seqtk - /usr/local/bin/seqtk
[07:42:55] Found parallel - /usr/local/bin/parallel
[07:42:55] Found freebayes - /usr/local/bin/freebayes
[07:42:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:55] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:55] Found gzip - /bin/gzip
[07:42:55] Found vt - /usr/local/bin/vt
[07:42:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:49:02] This is snippy 4.6.0Show full stderr[07:49:02] This is snippy 4.6.0
[07:49:02] Written by Torsten Seemann
[07:49:02] Obtained from https://github.com/tseemann/snippy
[07:49:02] Detected operating system: linux
[07:49:02] Enabling bundled linux tools.
[07:49:02] Found bwa - /usr/local/bin/bwa
[07:49:02] Found bcftools - /usr/local/bin/bcftools
[07:49:02] Found samtools - /usr/local/bin/samtools
[07:49:02] Found java - /usr/local/bin/java
[07:49:02] Found snpEff - /usr/local/bin/snpEff
[07:49:02] Found samclip - /usr/local/bin/samclip
[07:49:02] Found seqtk - /usr/local/bin/seqtk
[07:49:02] Found parallel - /usr/local/bin/parallel
[07:49:02] Found freebayes - /usr/local/bin/freebayes
[07:49:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:49:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:49:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:49:02] Found vcfuniq - /usr/local/bin/vcfuniq
[07:49:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:49:02] Found gzip - /bin/gzip
[07:49:02] Found vt - /usr/local/bin/vt
[07:49:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:49:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:49:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:49:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:49:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:49:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:49:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:49:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:49:19] This is snippy 4.6.0Show full stderr[07:49:19] This is snippy 4.6.0
[07:49:19] Written by Torsten Seemann
[07:49:19] Obtained from https://github.com/tseemann/snippy
[07:49:19] Detected operating system: linux
[07:49:19] Enabling bundled linux tools.
[07:49:19] Found bwa - /usr/local/bin/bwa
[07:49:19] Found bcftools - /usr/local/bin/bcftools
[07:49:19] Found samtools - /usr/local/bin/samtools
[07:49:19] Found java - /usr/local/bin/java
[07:49:19] Found snpEff - /usr/local/bin/snpEff
[07:49:19] Found samclip - /usr/local/bin/samclip
[07:49:19] Found seqtk - /usr/local/bin/seqtk
[07:49:19] Found parallel - /usr/local/bin/parallel
[07:49:19] Found freebayes - /usr/local/bin/freebayes
[07:49:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:49:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:49:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:49:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:49:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:49:19] Found gzip - /bin/gzip
[07:49:19] Found vt - /usr/local/bin/vt
[07:49:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:49:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:49:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:49:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:49:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:49:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:49:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:49:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:49:34] This is snippy 4.6.0Show full stderr[07:49:34] This is snippy 4.6.0
[07:49:34] Written by Torsten Seemann
[07:49:34] Obtained from https://github.com/tseemann/snippy
[07:49:34] Detected operating system: linux
[07:49:34] Enabling bundled linux tools.
[07:49:34] Found bwa - /usr/local/bin/bwa
[07:49:34] Found bcftools - /usr/local/bin/bcftools
[07:49:34] Found samtools - /usr/local/bin/samtools
[07:49:34] Found java - /usr/local/bin/java
[07:49:34] Found snpEff - /usr/local/bin/snpEff
[07:49:34] Found samclip - /usr/local/bin/samclip
[07:49:34] Found seqtk - /usr/local/bin/seqtk
[07:49:34] Found parallel - /usr/local/bin/parallel
[07:49:34] Found freebayes - /usr/local/bin/freebayes
[07:49:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:49:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:49:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:49:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:49:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:49:34] Found gzip - /bin/gzip
[07:49:34] Found vt - /usr/local/bin/vt
[07:49:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:49:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:49:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:49:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:49:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:49:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:49:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:49:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [07:46:01] This is snippy 4.6.0Show full stderr[07:46:01] This is snippy 4.6.0
[07:46:01] Written by Torsten Seemann
[07:46:01] Obtained from https://github.com/tseemann/snippy
[07:46:01] Detected operating system: linux
[07:46:01] Enabling bundled linux tools.
[07:46:01] Found bwa - /usr/local/bin/bwa
[07:46:01] Found bcftools - /usr/local/bin/bcftools
[07:46:01] Found samtools - /usr/local/bin/samtools
[07:46:01] Found java - /usr/local/bin/java
[07:46:01] Found snpEff - /usr/local/bin/snpEff
[07:46:01] Found samclip - /usr/local/bin/samclip
[07:46:01] Found seqtk - /usr/local/bin/seqtk
[07:46:01] Found parallel - /usr/local/bin/parallel
[07:46:01] Found freebayes - /usr/local/bin/freebayes
[07:46:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:01] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:01] Found gzip - /bin/gzip
[07:46:01] Found vt - /usr/local/bin/vt
[07:46:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [09:18:44] This is snippy 4.6.0Show full stderr[09:18:44] This is snippy 4.6.0
[09:18:44] Written by Torsten Seemann
[09:18:44] Obtained from https://github.com/tseemann/snippy
[09:18:44] Detected operating system: linux
[09:18:44] Enabling bundled linux tools.
[09:18:44] Found bwa - /usr/local/bin/bwa
[09:18:44] Found bcftools - /usr/local/bin/bcftools
[09:18:44] Found samtools - /usr/local/bin/samtools
[09:18:44] Found java - /usr/local/bin/java
[09:18:44] Found snpEff - /usr/local/bin/snpEff
[09:18:44] Found samclip - /usr/local/bin/samclip
[09:18:44] Found seqtk - /usr/local/bin/seqtk
[09:18:44] Found parallel - /usr/local/bin/parallel
[09:18:44] Found freebayes - /usr/local/bin/freebayes
[09:18:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:18:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:18:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:18:45] Found vcfuniq - /usr/local/bin/vcfuniq
[09:18:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:18:45] Found gzip - /bin/gzip
[09:18:45] Found vt - /usr/local/bin/vt
[09:18:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:18:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:18:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:18:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:18:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:18:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:18:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:18:45] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:18:51] Treating reference as 'fasta' format.
[09:18:51] Will use 1 CPU cores.
[09:18:51] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:18:51] Using read file: /corral4/main/objects/e/5/6/dataset_e56285d3-c227-475c-8ad7-daa6925b1921.dat
[09:18:51] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:18:51] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:18:51] Creating reference folder: reference
[09:18:51] Extracting FASTA and GFF from reference.
[09:18:59] Wrote 702 sequences to ref.fa
[09:18:59] Wrote 0 features to ref.gff
[09:18:59] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[09:18:59] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:18:59] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:18:59] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 2 | [09:20:50] This is snippy 4.6.0Show full stderr[09:20:50] This is snippy 4.6.0
[09:20:50] Written by Torsten Seemann
[09:20:50] Obtained from https://github.com/tseemann/snippy
[09:20:50] Detected operating system: linux
[09:20:50] Enabling bundled linux tools.
[09:20:50] Found bwa - /usr/local/bin/bwa
[09:20:50] Found bcftools - /usr/local/bin/bcftools
[09:20:50] Found samtools - /usr/local/bin/samtools
[09:20:50] Found java - /usr/local/bin/java
[09:20:50] Found snpEff - /usr/local/bin/snpEff
[09:20:50] Found samclip - /usr/local/bin/samclip
[09:20:50] Found seqtk - /usr/local/bin/seqtk
[09:20:50] Found parallel - /usr/local/bin/parallel
[09:20:50] Found freebayes - /usr/local/bin/freebayes
[09:20:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:20:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:20:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:20:50] Found vcfuniq - /usr/local/bin/vcfuniq
[09:20:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:20:50] Found gzip - /bin/gzip
[09:20:50] Found vt - /usr/local/bin/vt
[09:20:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:20:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:20:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:20:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:20:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:20:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:20:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:20:50] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:20:51] Treating reference as 'fasta' format.
[09:20:51] Will use 1 CPU cores.
[09:20:51] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:20:51] Using read file: /corral4/main/objects/8/9/d/dataset_89d88cd8-c878-453e-bdcb-ac6b4370d21b.dat
[09:20:51] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:20:51] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:20:51] Creating reference folder: reference
[09:20:51] Extracting FASTA and GFF from reference.
[09:20:58] Wrote 702 sequences to ref.fa
[09:20:58] Wrote 0 features to ref.gff
[09:20:59] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time.
[09:20:59] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:20:59] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:20:59] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 2 | [09:19:11] This is snippy 4.6.0Show full stderr[09:19:11] This is snippy 4.6.0
[09:19:11] Written by Torsten Seemann
[09:19:11] Obtained from https://github.com/tseemann/snippy
[09:19:11] Detected operating system: linux
[09:19:11] Enabling bundled linux tools.
[09:19:11] Found bwa - /usr/local/bin/bwa
[09:19:11] Found bcftools - /usr/local/bin/bcftools
[09:19:11] Found samtools - /usr/local/bin/samtools
[09:19:11] Found java - /usr/local/bin/java
[09:19:11] Found snpEff - /usr/local/bin/snpEff
[09:19:11] Found samclip - /usr/local/bin/samclip
[09:19:11] Found seqtk - /usr/local/bin/seqtk
[09:19:11] Found parallel - /usr/local/bin/parallel
[09:19:11] Found freebayes - /usr/local/bin/freebayes
[09:19:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:19:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:19:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:19:11] Found vcfuniq - /usr/local/bin/vcfuniq
[09:19:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:19:11] Found gzip - /bin/gzip
[09:19:11] Found vt - /usr/local/bin/vt
[09:19:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:19:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:19:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:19:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:19:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:19:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:19:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:19:12] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:19:13] Treating reference as 'fasta' format.
[09:19:13] Will use 1 CPU cores.
[09:19:13] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:19:13] Using read file: /corral4/main/objects/2/6/8/dataset_268e6c58-daba-4d88-a64e-3107304c568d.dat
[09:19:13] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:19:13] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:19:13] Creating reference folder: reference
[09:19:13] Extracting FASTA and GFF from reference.
[09:19:20] Wrote 702 sequences to ref.fa
[09:19:20] Wrote 0 features to ref.gff
[09:19:21] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[09:19:21] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:19:21] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:19:21] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 2 | [09:19:10] This is snippy 4.6.0Show full stderr[09:19:10] This is snippy 4.6.0
[09:19:10] Written by Torsten Seemann
[09:19:10] Obtained from https://github.com/tseemann/snippy
[09:19:10] Detected operating system: linux
[09:19:10] Enabling bundled linux tools.
[09:19:10] Found bwa - /usr/local/bin/bwa
[09:19:10] Found bcftools - /usr/local/bin/bcftools
[09:19:10] Found samtools - /usr/local/bin/samtools
[09:19:10] Found java - /usr/local/bin/java
[09:19:10] Found snpEff - /usr/local/bin/snpEff
[09:19:10] Found samclip - /usr/local/bin/samclip
[09:19:10] Found seqtk - /usr/local/bin/seqtk
[09:19:10] Found parallel - /usr/local/bin/parallel
[09:19:10] Found freebayes - /usr/local/bin/freebayes
[09:19:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:19:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:19:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:19:11] Found vcfuniq - /usr/local/bin/vcfuniq
[09:19:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:19:11] Found gzip - /bin/gzip
[09:19:11] Found vt - /usr/local/bin/vt
[09:19:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:19:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:19:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:19:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:19:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:19:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:19:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:19:11] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:19:12] Treating reference as 'fasta' format.
[09:19:12] Will use 1 CPU cores.
[09:19:12] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:19:12] Using read file: /corral4/main/objects/f/d/8/dataset_fd86cbff-ece5-4b83-858e-002d4b59aca9.dat
[09:19:12] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:19:12] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:19:12] Creating reference folder: reference
[09:19:12] Extracting FASTA and GFF from reference.
[09:19:19] Wrote 702 sequences to ref.fa
[09:19:19] Wrote 0 features to ref.gff
[09:19:19] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[09:19:19] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:19:20] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:19:20] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 2 | [09:20:47] This is snippy 4.6.0Show full stderr[09:20:47] This is snippy 4.6.0
[09:20:47] Written by Torsten Seemann
[09:20:47] Obtained from https://github.com/tseemann/snippy
[09:20:47] Detected operating system: linux
[09:20:47] Enabling bundled linux tools.
[09:20:47] Found bwa - /usr/local/bin/bwa
[09:20:47] Found bcftools - /usr/local/bin/bcftools
[09:20:47] Found samtools - /usr/local/bin/samtools
[09:20:47] Found java - /usr/local/bin/java
[09:20:47] Found snpEff - /usr/local/bin/snpEff
[09:20:47] Found samclip - /usr/local/bin/samclip
[09:20:47] Found seqtk - /usr/local/bin/seqtk
[09:20:47] Found parallel - /usr/local/bin/parallel
[09:20:47] Found freebayes - /usr/local/bin/freebayes
[09:20:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:20:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:20:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:20:47] Found vcfuniq - /usr/local/bin/vcfuniq
[09:20:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:20:47] Found gzip - /bin/gzip
[09:20:47] Found vt - /usr/local/bin/vt
[09:20:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:20:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:20:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:20:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:20:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:20:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:20:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:20:48] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:20:48] Treating reference as 'fasta' format.
[09:20:48] Will use 1 CPU cores.
[09:20:48] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:20:48] Using read file: /corral4/main/objects/d/0/b/dataset_d0b338bf-adde-498e-a96d-aa7ff4919c6d.dat
[09:20:48] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:20:48] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:20:48] Creating reference folder: reference
[09:20:48] Extracting FASTA and GFF from reference.
[09:20:57] Wrote 702 sequences to ref.fa
[09:20:57] Wrote 0 features to ref.gff
[09:20:57] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[09:20:57] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:20:57] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:20:57] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 2 | [09:22:04] This is snippy 4.6.0Show full stderr[09:22:04] This is snippy 4.6.0
[09:22:04] Written by Torsten Seemann
[09:22:04] Obtained from https://github.com/tseemann/snippy
[09:22:04] Detected operating system: linux
[09:22:04] Enabling bundled linux tools.
[09:22:04] Found bwa - /usr/local/bin/bwa
[09:22:04] Found bcftools - /usr/local/bin/bcftools
[09:22:04] Found samtools - /usr/local/bin/samtools
[09:22:04] Found java - /usr/local/bin/java
[09:22:04] Found snpEff - /usr/local/bin/snpEff
[09:22:04] Found samclip - /usr/local/bin/samclip
[09:22:04] Found seqtk - /usr/local/bin/seqtk
[09:22:04] Found parallel - /usr/local/bin/parallel
[09:22:04] Found freebayes - /usr/local/bin/freebayes
[09:22:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:22:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:22:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:22:04] Found vcfuniq - /usr/local/bin/vcfuniq
[09:22:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:22:04] Found gzip - /bin/gzip
[09:22:04] Found vt - /usr/local/bin/vt
[09:22:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:22:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:22:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:22:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:22:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:22:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:22:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:22:05] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:22:06] Treating reference as 'fasta' format.
[09:22:06] Will use 1 CPU cores.
[09:22:06] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:22:06] Using read file: /corral4/main/objects/5/4/d/dataset_54d0ab2a-0024-45c4-9d28-8ab9bed0a92d.dat
[09:22:06] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:22:06] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:22:06] Creating reference folder: reference
[09:22:06] Extracting FASTA and GFF from reference.
[09:22:14] Wrote 702 sequences to ref.fa
[09:22:14] Wrote 0 features to ref.gff
[09:22:14] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time.
[09:22:14] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:22:14] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:22:15] Running: bwa index reference/ref.fa 2>> snps.log
[09:27:58] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:27:58] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 2 | [09:21:41] This is snippy 4.6.0Show full stderr[09:21:41] This is snippy 4.6.0
[09:21:41] Written by Torsten Seemann
[09:21:41] Obtained from https://github.com/tseemann/snippy
[09:21:41] Detected operating system: linux
[09:21:41] Enabling bundled linux tools.
[09:21:41] Found bwa - /usr/local/bin/bwa
[09:21:41] Found bcftools - /usr/local/bin/bcftools
[09:21:41] Found samtools - /usr/local/bin/samtools
[09:21:41] Found java - /usr/local/bin/java
[09:21:41] Found snpEff - /usr/local/bin/snpEff
[09:21:41] Found samclip - /usr/local/bin/samclip
[09:21:41] Found seqtk - /usr/local/bin/seqtk
[09:21:41] Found parallel - /usr/local/bin/parallel
[09:21:41] Found freebayes - /usr/local/bin/freebayes
[09:21:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:21:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:21:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:21:41] Found vcfuniq - /usr/local/bin/vcfuniq
[09:21:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:21:41] Found gzip - /bin/gzip
[09:21:41] Found vt - /usr/local/bin/vt
[09:21:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:21:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:21:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:21:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:21:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:21:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:21:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:21:42] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:21:43] Treating reference as 'fasta' format.
[09:21:43] Will use 1 CPU cores.
[09:21:43] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:21:43] Using read file: /corral4/main/objects/8/1/7/dataset_817afe11-36e0-49b9-9e4f-ff9727bd156d.dat
[09:21:43] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:43] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:43] Creating reference folder: reference
[09:21:43] Extracting FASTA and GFF from reference.
[09:21:50] Wrote 702 sequences to ref.fa
[09:21:50] Wrote 0 features to ref.gff
[09:21:51] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[09:21:51] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:51] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:21:51] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 2 | [13:10:17] This is snippy 4.6.0Show full stderr[13:10:17] This is snippy 4.6.0
[13:10:17] Written by Torsten Seemann
[13:10:17] Obtained from https://github.com/tseemann/snippy
[13:10:17] Detected operating system: linux
[13:10:17] Enabling bundled linux tools.
[13:10:17] Found bwa - /usr/local/bin/bwa
[13:10:17] Found bcftools - /usr/local/bin/bcftools
[13:10:17] Found samtools - /usr/local/bin/samtools
[13:10:17] Found java - /usr/local/bin/java
[13:10:17] Found snpEff - /usr/local/bin/snpEff
[13:10:18] Found samclip - /usr/local/bin/samclip
[13:10:18] Found seqtk - /usr/local/bin/seqtk
[13:10:18] Found parallel - /usr/local/bin/parallel
[13:10:18] Found freebayes - /usr/local/bin/freebayes
[13:10:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:10:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:10:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:10:18] Found vcfuniq - /usr/local/bin/vcfuniq
[13:10:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:10:18] Found gzip - /bin/gzip
[13:10:18] Found vt - /usr/local/bin/vt
[13:10:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:10:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:10:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:10:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:10:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:10:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:10:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:10:18] Using reference: /jetstream2/scratch/main/jobs/72274633/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat
[13:10:18] Treating reference as 'fasta' format.
[13:10:18] Will use 1 CPU cores.
[13:10:18] Using read file: /jetstream2/scratch/main/jobs/72274633/inputs/dataset_937e13a3-f031-450e-ba32-5b187a6037b7.dat
[13:10:18] Creating folder: Select_on_dataset_16
[13:10:18] Changing working directory: Select_on_dataset_16
[13:10:18] Creating reference folder: reference
[13:10:18] Extracting FASTA and GFF from reference.
[13:10:19] Wrote 3 sequences to ref.fa
[13:10:19] Wrote 0 features to ref.gff
[13:10:19] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[13:10:19] Using BAM RG (Read Group) ID: Select_on_dataset_16
[13:10:19] Running: samtools faidx reference/ref.fa 2>> snps.log
[13:10:19] Running: bwa index reference/ref.fa 2>> snps.log
[13:10:21] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[13:10:22] Running: ln -sf reference/ref.fa . 2>> snps.log
[13:10:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[13:10:22] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[13:10:22] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_16\tSM:Select_on_dataset_16' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72274633/inputs/dataset_937e13a3-f031-450e-ba32-5b187a6037b7.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72274633/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72274633/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72274633/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::process] read 1 sequences (12466108 bp)...
[M::mem_process_seqs] Processed |
| 2 | [12:50:26] This is snippy 4.6.0Show full stderr[12:50:26] This is snippy 4.6.0
[12:50:26] Written by Torsten Seemann
[12:50:26] Obtained from https://github.com/tseemann/snippy
[12:50:26] Detected operating system: linux
[12:50:26] Enabling bundled linux tools.
[12:50:26] Found bwa - /usr/local/bin/bwa
[12:50:26] Found bcftools - /usr/local/bin/bcftools
[12:50:26] Found samtools - /usr/local/bin/samtools
[12:50:26] Found java - /usr/local/bin/java
[12:50:26] Found snpEff - /usr/local/bin/snpEff
[12:50:26] Found samclip - /usr/local/bin/samclip
[12:50:26] Found seqtk - /usr/local/bin/seqtk
[12:50:26] Found parallel - /usr/local/bin/parallel
[12:50:26] Found freebayes - /usr/local/bin/freebayes
[12:50:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:50:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:50:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:50:26] Found vcfuniq - /usr/local/bin/vcfuniq
[12:50:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:50:26] Found gzip - /bin/gzip
[12:50:26] Found vt - /usr/local/bin/vt
[12:50:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:50:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:50:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:50:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:50:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:50:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:50:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:50:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:48:17] This is snippy 4.6.0Show full stderr[12:48:17] This is snippy 4.6.0
[12:48:17] Written by Torsten Seemann
[12:48:17] Obtained from https://github.com/tseemann/snippy
[12:48:17] Detected operating system: linux
[12:48:17] Enabling bundled linux tools.
[12:48:17] Found bwa - /usr/local/bin/bwa
[12:48:17] Found bcftools - /usr/local/bin/bcftools
[12:48:17] Found samtools - /usr/local/bin/samtools
[12:48:17] Found java - /usr/local/bin/java
[12:48:17] Found snpEff - /usr/local/bin/snpEff
[12:48:17] Found samclip - /usr/local/bin/samclip
[12:48:17] Found seqtk - /usr/local/bin/seqtk
[12:48:17] Found parallel - /usr/local/bin/parallel
[12:48:17] Found freebayes - /usr/local/bin/freebayes
[12:48:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:48:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:48:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:48:17] Found vcfuniq - /usr/local/bin/vcfuniq
[12:48:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:48:17] Found gzip - /bin/gzip
[12:48:17] Found vt - /usr/local/bin/vt
[12:48:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:48:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:48:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:48:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:48:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:48:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:48:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:48:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:49:55] This is snippy 4.6.0Show full stderr[12:49:55] This is snippy 4.6.0
[12:49:55] Written by Torsten Seemann
[12:49:55] Obtained from https://github.com/tseemann/snippy
[12:49:55] Detected operating system: linux
[12:49:55] Enabling bundled linux tools.
[12:49:55] Found bwa - /usr/local/bin/bwa
[12:49:55] Found bcftools - /usr/local/bin/bcftools
[12:49:55] Found samtools - /usr/local/bin/samtools
[12:49:55] Found java - /usr/local/bin/java
[12:49:55] Found snpEff - /usr/local/bin/snpEff
[12:49:55] Found samclip - /usr/local/bin/samclip
[12:49:55] Found seqtk - /usr/local/bin/seqtk
[12:49:55] Found parallel - /usr/local/bin/parallel
[12:49:55] Found freebayes - /usr/local/bin/freebayes
[12:49:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:49:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:49:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:49:55] Found vcfuniq - /usr/local/bin/vcfuniq
[12:49:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:49:55] Found gzip - /bin/gzip
[12:49:55] Found vt - /usr/local/bin/vt
[12:49:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:49:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:49:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:49:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:49:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:49:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:49:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:49:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:52:20] This is snippy 4.6.0Show full stderr[12:52:20] This is snippy 4.6.0
[12:52:20] Written by Torsten Seemann
[12:52:20] Obtained from https://github.com/tseemann/snippy
[12:52:20] Detected operating system: linux
[12:52:20] Enabling bundled linux tools.
[12:52:20] Found bwa - /usr/local/bin/bwa
[12:52:20] Found bcftools - /usr/local/bin/bcftools
[12:52:20] Found samtools - /usr/local/bin/samtools
[12:52:20] Found java - /usr/local/bin/java
[12:52:20] Found snpEff - /usr/local/bin/snpEff
[12:52:20] Found samclip - /usr/local/bin/samclip
[12:52:20] Found seqtk - /usr/local/bin/seqtk
[12:52:20] Found parallel - /usr/local/bin/parallel
[12:52:20] Found freebayes - /usr/local/bin/freebayes
[12:52:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:52:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:52:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:52:20] Found vcfuniq - /usr/local/bin/vcfuniq
[12:52:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:52:20] Found gzip - /bin/gzip
[12:52:20] Found vt - /usr/local/bin/vt
[12:52:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:52:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:52:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:52:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:52:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:52:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:52:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:52:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:57:03] This is snippy 4.6.0Show full stderr[12:57:03] This is snippy 4.6.0
[12:57:03] Written by Torsten Seemann
[12:57:03] Obtained from https://github.com/tseemann/snippy
[12:57:03] Detected operating system: linux
[12:57:03] Enabling bundled linux tools.
[12:57:03] Found bwa - /usr/local/bin/bwa
[12:57:03] Found bcftools - /usr/local/bin/bcftools
[12:57:03] Found samtools - /usr/local/bin/samtools
[12:57:03] Found java - /usr/local/bin/java
[12:57:03] Found snpEff - /usr/local/bin/snpEff
[12:57:03] Found samclip - /usr/local/bin/samclip
[12:57:03] Found seqtk - /usr/local/bin/seqtk
[12:57:03] Found parallel - /usr/local/bin/parallel
[12:57:03] Found freebayes - /usr/local/bin/freebayes
[12:57:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:03] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:03] Found gzip - /bin/gzip
[12:57:03] Found vt - /usr/local/bin/vt
[12:57:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:54:13] This is snippy 4.6.0Show full stderr[12:54:13] This is snippy 4.6.0
[12:54:13] Written by Torsten Seemann
[12:54:13] Obtained from https://github.com/tseemann/snippy
[12:54:13] Detected operating system: linux
[12:54:13] Enabling bundled linux tools.
[12:54:13] Found bwa - /usr/local/bin/bwa
[12:54:13] Found bcftools - /usr/local/bin/bcftools
[12:54:13] Found samtools - /usr/local/bin/samtools
[12:54:13] Found java - /usr/local/bin/java
[12:54:13] Found snpEff - /usr/local/bin/snpEff
[12:54:13] Found samclip - /usr/local/bin/samclip
[12:54:13] Found seqtk - /usr/local/bin/seqtk
[12:54:13] Found parallel - /usr/local/bin/parallel
[12:54:13] Found freebayes - /usr/local/bin/freebayes
[12:54:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:54:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:54:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:54:13] Found vcfuniq - /usr/local/bin/vcfuniq
[12:54:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:54:13] Found gzip - /bin/gzip
[12:54:13] Found vt - /usr/local/bin/vt
[12:54:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:54:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:54:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:54:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:54:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:54:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:54:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:54:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:58:11] This is snippy 4.6.0Show full stderr[12:58:11] This is snippy 4.6.0
[12:58:11] Written by Torsten Seemann
[12:58:11] Obtained from https://github.com/tseemann/snippy
[12:58:11] Detected operating system: linux
[12:58:11] Enabling bundled linux tools.
[12:58:11] Found bwa - /usr/local/bin/bwa
[12:58:11] Found bcftools - /usr/local/bin/bcftools
[12:58:11] Found samtools - /usr/local/bin/samtools
[12:58:11] Found java - /usr/local/bin/java
[12:58:11] Found snpEff - /usr/local/bin/snpEff
[12:58:11] Found samclip - /usr/local/bin/samclip
[12:58:11] Found seqtk - /usr/local/bin/seqtk
[12:58:11] Found parallel - /usr/local/bin/parallel
[12:58:11] Found freebayes - /usr/local/bin/freebayes
[12:58:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:58:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:58:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:58:11] Found vcfuniq - /usr/local/bin/vcfuniq
[12:58:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:58:11] Found gzip - /bin/gzip
[12:58:11] Found vt - /usr/local/bin/vt
[12:58:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:58:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:58:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:58:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:58:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:58:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:58:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:58:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:54:57] This is snippy 4.6.0Show full stderr[12:54:57] This is snippy 4.6.0
[12:54:57] Written by Torsten Seemann
[12:54:57] Obtained from https://github.com/tseemann/snippy
[12:54:57] Detected operating system: linux
[12:54:57] Enabling bundled linux tools.
[12:54:57] Found bwa - /usr/local/bin/bwa
[12:54:57] Found bcftools - /usr/local/bin/bcftools
[12:54:57] Found samtools - /usr/local/bin/samtools
[12:54:57] Found java - /usr/local/bin/java
[12:54:57] Found snpEff - /usr/local/bin/snpEff
[12:54:57] Found samclip - /usr/local/bin/samclip
[12:54:57] Found seqtk - /usr/local/bin/seqtk
[12:54:57] Found parallel - /usr/local/bin/parallel
[12:54:57] Found freebayes - /usr/local/bin/freebayes
[12:54:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:54:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:54:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:54:57] Found vcfuniq - /usr/local/bin/vcfuniq
[12:54:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:54:57] Found gzip - /bin/gzip
[12:54:57] Found vt - /usr/local/bin/vt
[12:54:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:54:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:54:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:54:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:54:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:54:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:54:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:54:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:57:43] This is snippy 4.6.0Show full stderr[12:57:43] This is snippy 4.6.0
[12:57:43] Written by Torsten Seemann
[12:57:43] Obtained from https://github.com/tseemann/snippy
[12:57:43] Detected operating system: linux
[12:57:43] Enabling bundled linux tools.
[12:57:43] Found bwa - /usr/local/bin/bwa
[12:57:43] Found bcftools - /usr/local/bin/bcftools
[12:57:43] Found samtools - /usr/local/bin/samtools
[12:57:43] Found java - /usr/local/bin/java
[12:57:43] Found snpEff - /usr/local/bin/snpEff
[12:57:43] Found samclip - /usr/local/bin/samclip
[12:57:43] Found seqtk - /usr/local/bin/seqtk
[12:57:43] Found parallel - /usr/local/bin/parallel
[12:57:43] Found freebayes - /usr/local/bin/freebayes
[12:57:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:43] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:43] Found gzip - /bin/gzip
[12:57:43] Found vt - /usr/local/bin/vt
[12:57:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [13:04:15] This is snippy 4.6.0Show full stderr[13:04:15] This is snippy 4.6.0
[13:04:15] Written by Torsten Seemann
[13:04:15] Obtained from https://github.com/tseemann/snippy
[13:04:15] Detected operating system: linux
[13:04:15] Enabling bundled linux tools.
[13:04:15] Found bwa - /usr/local/bin/bwa
[13:04:15] Found bcftools - /usr/local/bin/bcftools
[13:04:15] Found samtools - /usr/local/bin/samtools
[13:04:15] Found java - /usr/local/bin/java
[13:04:15] Found snpEff - /usr/local/bin/snpEff
[13:04:15] Found samclip - /usr/local/bin/samclip
[13:04:15] Found seqtk - /usr/local/bin/seqtk
[13:04:15] Found parallel - /usr/local/bin/parallel
[13:04:15] Found freebayes - /usr/local/bin/freebayes
[13:04:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:04:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:04:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:04:15] Found vcfuniq - /usr/local/bin/vcfuniq
[13:04:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:04:15] Found gzip - /bin/gzip
[13:04:15] Found vt - /usr/local/bin/vt
[13:04:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:04:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:04:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:04:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:04:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:04:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:04:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:04:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [13:30:33] This is snippy 4.6.0Show full stderr[13:30:33] This is snippy 4.6.0
[13:30:33] Written by Torsten Seemann
[13:30:33] Obtained from https://github.com/tseemann/snippy
[13:30:33] Detected operating system: linux
[13:30:33] Enabling bundled linux tools.
[13:30:33] Found bwa - /usr/local/bin/bwa
[13:30:33] Found bcftools - /usr/local/bin/bcftools
[13:30:33] Found samtools - /usr/local/bin/samtools
[13:30:33] Found java - /usr/local/bin/java
[13:30:33] Found snpEff - /usr/local/bin/snpEff
[13:30:33] Found samclip - /usr/local/bin/samclip
[13:30:33] Found seqtk - /usr/local/bin/seqtk
[13:30:33] Found parallel - /usr/local/bin/parallel
[13:30:33] Found freebayes - /usr/local/bin/freebayes
[13:30:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:30:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:30:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:30:33] Found vcfuniq - /usr/local/bin/vcfuniq
[13:30:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:30:33] Found gzip - /bin/gzip
[13:30:33] Found vt - /usr/local/bin/vt
[13:30:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:30:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:30:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:30:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:30:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:30:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:30:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:30:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:51:27] This is snippy 4.6.0Show full stderr[12:51:27] This is snippy 4.6.0
[12:51:27] Written by Torsten Seemann
[12:51:27] Obtained from https://github.com/tseemann/snippy
[12:51:27] Detected operating system: linux
[12:51:27] Enabling bundled linux tools.
[12:51:27] Found bwa - /usr/local/bin/bwa
[12:51:27] Found bcftools - /usr/local/bin/bcftools
[12:51:27] Found samtools - /usr/local/bin/samtools
[12:51:27] Found java - /usr/local/bin/java
[12:51:27] Found snpEff - /usr/local/bin/snpEff
[12:51:27] Found samclip - /usr/local/bin/samclip
[12:51:27] Found seqtk - /usr/local/bin/seqtk
[12:51:27] Found parallel - /usr/local/bin/parallel
[12:51:27] Found freebayes - /usr/local/bin/freebayes
[12:51:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:51:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:51:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:51:27] Found vcfuniq - /usr/local/bin/vcfuniq
[12:51:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:51:27] Found gzip - /bin/gzip
[12:51:27] Found vt - /usr/local/bin/vt
[12:51:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:51:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:51:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:51:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:51:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:51:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:51:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:51:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:52:07] This is snippy 4.6.0Show full stderr[12:52:07] This is snippy 4.6.0
[12:52:07] Written by Torsten Seemann
[12:52:07] Obtained from https://github.com/tseemann/snippy
[12:52:07] Detected operating system: linux
[12:52:07] Enabling bundled linux tools.
[12:52:07] Found bwa - /usr/local/bin/bwa
[12:52:07] Found bcftools - /usr/local/bin/bcftools
[12:52:07] Found samtools - /usr/local/bin/samtools
[12:52:07] Found java - /usr/local/bin/java
[12:52:07] Found snpEff - /usr/local/bin/snpEff
[12:52:07] Found samclip - /usr/local/bin/samclip
[12:52:07] Found seqtk - /usr/local/bin/seqtk
[12:52:07] Found parallel - /usr/local/bin/parallel
[12:52:07] Found freebayes - /usr/local/bin/freebayes
[12:52:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:52:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:52:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:52:07] Found vcfuniq - /usr/local/bin/vcfuniq
[12:52:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:52:07] Found gzip - /bin/gzip
[12:52:07] Found vt - /usr/local/bin/vt
[12:52:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:52:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:52:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:52:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:52:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:52:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:52:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:52:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:52:35] This is snippy 4.6.0Show full stderr[12:52:35] This is snippy 4.6.0
[12:52:35] Written by Torsten Seemann
[12:52:35] Obtained from https://github.com/tseemann/snippy
[12:52:35] Detected operating system: linux
[12:52:35] Enabling bundled linux tools.
[12:52:35] Found bwa - /usr/local/bin/bwa
[12:52:35] Found bcftools - /usr/local/bin/bcftools
[12:52:35] Found samtools - /usr/local/bin/samtools
[12:52:35] Found java - /usr/local/bin/java
[12:52:35] Found snpEff - /usr/local/bin/snpEff
[12:52:35] Found samclip - /usr/local/bin/samclip
[12:52:35] Found seqtk - /usr/local/bin/seqtk
[12:52:35] Found parallel - /usr/local/bin/parallel
[12:52:35] Found freebayes - /usr/local/bin/freebayes
[12:52:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:52:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:52:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:52:35] Found vcfuniq - /usr/local/bin/vcfuniq
[12:52:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:52:35] Found gzip - /bin/gzip
[12:52:35] Found vt - /usr/local/bin/vt
[12:52:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:52:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:52:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:52:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:52:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:52:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:52:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:52:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:57:57] This is snippy 4.6.0Show full stderr[12:57:57] This is snippy 4.6.0
[12:57:57] Written by Torsten Seemann
[12:57:57] Obtained from https://github.com/tseemann/snippy
[12:57:57] Detected operating system: linux
[12:57:57] Enabling bundled linux tools.
[12:57:57] Found bwa - /usr/local/bin/bwa
[12:57:57] Found bcftools - /usr/local/bin/bcftools
[12:57:57] Found samtools - /usr/local/bin/samtools
[12:57:57] Found java - /usr/local/bin/java
[12:57:57] Found snpEff - /usr/local/bin/snpEff
[12:57:57] Found samclip - /usr/local/bin/samclip
[12:57:57] Found seqtk - /usr/local/bin/seqtk
[12:57:57] Found parallel - /usr/local/bin/parallel
[12:57:57] Found freebayes - /usr/local/bin/freebayes
[12:57:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:57] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:57] Found gzip - /bin/gzip
[12:57:57] Found vt - /usr/local/bin/vt
[12:57:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:59:05] This is snippy 4.6.0Show full stderr[12:59:05] This is snippy 4.6.0
[12:59:05] Written by Torsten Seemann
[12:59:05] Obtained from https://github.com/tseemann/snippy
[12:59:05] Detected operating system: linux
[12:59:05] Enabling bundled linux tools.
[12:59:05] Found bwa - /usr/local/bin/bwa
[12:59:05] Found bcftools - /usr/local/bin/bcftools
[12:59:05] Found samtools - /usr/local/bin/samtools
[12:59:05] Found java - /usr/local/bin/java
[12:59:05] Found snpEff - /usr/local/bin/snpEff
[12:59:05] Found samclip - /usr/local/bin/samclip
[12:59:05] Found seqtk - /usr/local/bin/seqtk
[12:59:05] Found parallel - /usr/local/bin/parallel
[12:59:05] Found freebayes - /usr/local/bin/freebayes
[12:59:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:59:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:59:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:59:05] Found vcfuniq - /usr/local/bin/vcfuniq
[12:59:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:59:05] Found gzip - /bin/gzip
[12:59:05] Found vt - /usr/local/bin/vt
[12:59:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:59:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:59:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:59:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:59:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:59:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:59:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:59:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:59:21] This is snippy 4.6.0Show full stderr[12:59:21] This is snippy 4.6.0
[12:59:21] Written by Torsten Seemann
[12:59:21] Obtained from https://github.com/tseemann/snippy
[12:59:21] Detected operating system: linux
[12:59:21] Enabling bundled linux tools.
[12:59:21] Found bwa - /usr/local/bin/bwa
[12:59:21] Found bcftools - /usr/local/bin/bcftools
[12:59:21] Found samtools - /usr/local/bin/samtools
[12:59:21] Found java - /usr/local/bin/java
[12:59:21] Found snpEff - /usr/local/bin/snpEff
[12:59:21] Found samclip - /usr/local/bin/samclip
[12:59:21] Found seqtk - /usr/local/bin/seqtk
[12:59:21] Found parallel - /usr/local/bin/parallel
[12:59:21] Found freebayes - /usr/local/bin/freebayes
[12:59:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:59:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:59:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:59:21] Found vcfuniq - /usr/local/bin/vcfuniq
[12:59:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:59:21] Found gzip - /bin/gzip
[12:59:21] Found vt - /usr/local/bin/vt
[12:59:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:59:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:59:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:59:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:59:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:59:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:59:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:59:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:59:18] This is snippy 4.6.0Show full stderr[12:59:18] This is snippy 4.6.0
[12:59:18] Written by Torsten Seemann
[12:59:18] Obtained from https://github.com/tseemann/snippy
[12:59:18] Detected operating system: linux
[12:59:18] Enabling bundled linux tools.
[12:59:18] Found bwa - /usr/local/bin/bwa
[12:59:18] Found bcftools - /usr/local/bin/bcftools
[12:59:18] Found samtools - /usr/local/bin/samtools
[12:59:18] Found java - /usr/local/bin/java
[12:59:18] Found snpEff - /usr/local/bin/snpEff
[12:59:18] Found samclip - /usr/local/bin/samclip
[12:59:18] Found seqtk - /usr/local/bin/seqtk
[12:59:18] Found parallel - /usr/local/bin/parallel
[12:59:18] Found freebayes - /usr/local/bin/freebayes
[12:59:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:59:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:59:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:59:18] Found vcfuniq - /usr/local/bin/vcfuniq
[12:59:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:59:18] Found gzip - /bin/gzip
[12:59:18] Found vt - /usr/local/bin/vt
[12:59:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:59:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:59:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:59:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:59:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:59:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:59:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:59:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [12:59:49] This is snippy 4.6.0Show full stderr[12:59:49] This is snippy 4.6.0
[12:59:49] Written by Torsten Seemann
[12:59:49] Obtained from https://github.com/tseemann/snippy
[12:59:49] Detected operating system: linux
[12:59:49] Enabling bundled linux tools.
[12:59:49] Found bwa - /usr/local/bin/bwa
[12:59:49] Found bcftools - /usr/local/bin/bcftools
[12:59:49] Found samtools - /usr/local/bin/samtools
[12:59:49] Found java - /usr/local/bin/java
[12:59:49] Found snpEff - /usr/local/bin/snpEff
[12:59:49] Found samclip - /usr/local/bin/samclip
[12:59:49] Found seqtk - /usr/local/bin/seqtk
[12:59:49] Found parallel - /usr/local/bin/parallel
[12:59:49] Found freebayes - /usr/local/bin/freebayes
[12:59:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:59:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:59:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:59:49] Found vcfuniq - /usr/local/bin/vcfuniq
[12:59:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:59:49] Found gzip - /bin/gzip
[12:59:49] Found vt - /usr/local/bin/vt
[12:59:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:59:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:59:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:59:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:59:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:59:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:59:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:59:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [16:31:37] This is snippy 4.6.0Show full stderr[16:31:37] This is snippy 4.6.0
[16:31:37] Written by Torsten Seemann
[16:31:37] Obtained from https://github.com/tseemann/snippy
[16:31:37] Detected operating system: linux
[16:31:37] Enabling bundled linux tools.
[16:31:37] Found bwa - /usr/local/bin/bwa
[16:31:37] Found bcftools - /usr/local/bin/bcftools
[16:31:37] Found samtools - /usr/local/bin/samtools
[16:31:37] Found java - /usr/local/bin/java
[16:31:37] Found snpEff - /usr/local/bin/snpEff
[16:31:37] Found samclip - /usr/local/bin/samclip
[16:31:37] Found seqtk - /usr/local/bin/seqtk
[16:31:37] Found parallel - /usr/local/bin/parallel
[16:31:37] Found freebayes - /usr/local/bin/freebayes
[16:31:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:31:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:31:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:31:37] Found vcfuniq - /usr/local/bin/vcfuniq
[16:31:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:31:37] Found gzip - /bin/gzip
[16:31:37] Found vt - /usr/local/bin/vt
[16:31:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:31:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:31:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:31:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:31:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:31:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:31:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:31:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [19:40:28] This is snippy 4.6.0Show full stderr[19:40:28] This is snippy 4.6.0
[19:40:28] Written by Torsten Seemann
[19:40:28] Obtained from https://github.com/tseemann/snippy
[19:40:28] Detected operating system: linux
[19:40:28] Enabling bundled linux tools.
[19:40:28] Found bwa - /usr/local/bin/bwa
[19:40:28] Found bcftools - /usr/local/bin/bcftools
[19:40:28] Found samtools - /usr/local/bin/samtools
[19:40:28] Found java - /usr/local/bin/java
[19:40:28] Found snpEff - /usr/local/bin/snpEff
[19:40:28] Found samclip - /usr/local/bin/samclip
[19:40:28] Found seqtk - /usr/local/bin/seqtk
[19:40:28] Found parallel - /usr/local/bin/parallel
[19:40:28] Found freebayes - /usr/local/bin/freebayes
[19:40:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:28] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:28] Found gzip - /bin/gzip
[19:40:28] Found vt - /usr/local/bin/vt
[19:40:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [19:40:55] This is snippy 4.6.0Show full stderr[19:40:55] This is snippy 4.6.0
[19:40:55] Written by Torsten Seemann
[19:40:55] Obtained from https://github.com/tseemann/snippy
[19:40:55] Detected operating system: linux
[19:40:55] Enabling bundled linux tools.
[19:40:55] Found bwa - /usr/local/bin/bwa
[19:40:55] Found bcftools - /usr/local/bin/bcftools
[19:40:55] Found samtools - /usr/local/bin/samtools
[19:40:55] Found java - /usr/local/bin/java
[19:40:55] Found snpEff - /usr/local/bin/snpEff
[19:40:55] Found samclip - /usr/local/bin/samclip
[19:40:55] Found seqtk - /usr/local/bin/seqtk
[19:40:55] Found parallel - /usr/local/bin/parallel
[19:40:55] Found freebayes - /usr/local/bin/freebayes
[19:40:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:55] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:55] Found gzip - /bin/gzip
[19:40:55] Found vt - /usr/local/bin/vt
[19:40:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [19:40:47] This is snippy 4.6.0Show full stderr[19:40:47] This is snippy 4.6.0
[19:40:47] Written by Torsten Seemann
[19:40:47] Obtained from https://github.com/tseemann/snippy
[19:40:47] Detected operating system: linux
[19:40:47] Enabling bundled linux tools.
[19:40:47] Found bwa - /usr/local/bin/bwa
[19:40:47] Found bcftools - /usr/local/bin/bcftools
[19:40:47] Found samtools - /usr/local/bin/samtools
[19:40:47] Found java - /usr/local/bin/java
[19:40:47] Found snpEff - /usr/local/bin/snpEff
[19:40:47] Found samclip - /usr/local/bin/samclip
[19:40:47] Found seqtk - /usr/local/bin/seqtk
[19:40:47] Found parallel - /usr/local/bin/parallel
[19:40:47] Found freebayes - /usr/local/bin/freebayes
[19:40:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:47] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:47] Found gzip - /bin/gzip
[19:40:47] Found vt - /usr/local/bin/vt
[19:40:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [08:48:47] This is snippy 4.6.0Show full stderr[08:48:47] This is snippy 4.6.0
[08:48:47] Written by Torsten Seemann
[08:48:47] Obtained from https://github.com/tseemann/snippy
[08:48:47] Detected operating system: linux
[08:48:47] Enabling bundled linux tools.
[08:48:47] Found bwa - /usr/local/bin/bwa
[08:48:47] Found bcftools - /usr/local/bin/bcftools
[08:48:47] Found samtools - /usr/local/bin/samtools
[08:48:47] Found java - /usr/local/bin/java
[08:48:47] Found snpEff - /usr/local/bin/snpEff
[08:48:47] Found samclip - /usr/local/bin/samclip
[08:48:47] Found seqtk - /usr/local/bin/seqtk
[08:48:47] Found parallel - /usr/local/bin/parallel
[08:48:47] Found freebayes - /usr/local/bin/freebayes
[08:48:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:48:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:48:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:48:48] Found vcfuniq - /usr/local/bin/vcfuniq
[08:48:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:48:48] Found gzip - /bin/gzip
[08:48:48] Found vt - /usr/local/bin/vt
[08:48:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:48:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:48:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:48:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:48:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:48:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:48:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:48:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [09:02:02] This is snippy 4.6.0Show full stderr[09:02:02] This is snippy 4.6.0
[09:02:02] Written by Torsten Seemann
[09:02:02] Obtained from https://github.com/tseemann/snippy
[09:02:02] Detected operating system: linux
[09:02:02] Enabling bundled linux tools.
[09:02:02] Found bwa - /usr/local/bin/bwa
[09:02:02] Found bcftools - /usr/local/bin/bcftools
[09:02:02] Found samtools - /usr/local/bin/samtools
[09:02:02] Found java - /usr/local/bin/java
[09:02:02] Found snpEff - /usr/local/bin/snpEff
[09:02:02] Found samclip - /usr/local/bin/samclip
[09:02:02] Found seqtk - /usr/local/bin/seqtk
[09:02:02] Found parallel - /usr/local/bin/parallel
[09:02:02] Found freebayes - /usr/local/bin/freebayes
[09:02:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:02:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:02:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:02:02] Found vcfuniq - /usr/local/bin/vcfuniq
[09:02:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:02:02] Found gzip - /bin/gzip
[09:02:02] Found vt - /usr/local/bin/vt
[09:02:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:02:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:02:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:02:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:02:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:02:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:02:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:02:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:45:05] This is snippy 4.6.0Show full stderr[14:45:05] This is snippy 4.6.0
[14:45:05] Written by Torsten Seemann
[14:45:05] Obtained from https://github.com/tseemann/snippy
[14:45:05] Detected operating system: linux
[14:45:05] Enabling bundled linux tools.
[14:45:05] Found bwa - /usr/local/bin/bwa
[14:45:05] Found bcftools - /usr/local/bin/bcftools
[14:45:05] Found samtools - /usr/local/bin/samtools
[14:45:05] Found java - /usr/local/bin/java
[14:45:05] Found snpEff - /usr/local/bin/snpEff
[14:45:05] Found samclip - /usr/local/bin/samclip
[14:45:05] Found seqtk - /usr/local/bin/seqtk
[14:45:05] Found parallel - /usr/local/bin/parallel
[14:45:05] Found freebayes - /usr/local/bin/freebayes
[14:45:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:05] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:05] Found gzip - /bin/gzip
[14:45:05] Found vt - /usr/local/bin/vt
[14:45:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:45:18] This is snippy 4.6.0Show full stderr[14:45:18] This is snippy 4.6.0
[14:45:18] Written by Torsten Seemann
[14:45:18] Obtained from https://github.com/tseemann/snippy
[14:45:18] Detected operating system: linux
[14:45:18] Enabling bundled linux tools.
[14:45:18] Found bwa - /usr/local/bin/bwa
[14:45:18] Found bcftools - /usr/local/bin/bcftools
[14:45:18] Found samtools - /usr/local/bin/samtools
[14:45:18] Found java - /usr/local/bin/java
[14:45:18] Found snpEff - /usr/local/bin/snpEff
[14:45:18] Found samclip - /usr/local/bin/samclip
[14:45:18] Found seqtk - /usr/local/bin/seqtk
[14:45:18] Found parallel - /usr/local/bin/parallel
[14:45:18] Found freebayes - /usr/local/bin/freebayes
[14:45:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:18] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:18] Found gzip - /bin/gzip
[14:45:18] Found vt - /usr/local/bin/vt
[14:45:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:45:45] This is snippy 4.6.0Show full stderr[14:45:45] This is snippy 4.6.0
[14:45:45] Written by Torsten Seemann
[14:45:45] Obtained from https://github.com/tseemann/snippy
[14:45:45] Detected operating system: linux
[14:45:45] Enabling bundled linux tools.
[14:45:45] Found bwa - /usr/local/bin/bwa
[14:45:45] Found bcftools - /usr/local/bin/bcftools
[14:45:45] Found samtools - /usr/local/bin/samtools
[14:45:45] Found java - /usr/local/bin/java
[14:45:45] Found snpEff - /usr/local/bin/snpEff
[14:45:45] Found samclip - /usr/local/bin/samclip
[14:45:45] Found seqtk - /usr/local/bin/seqtk
[14:45:45] Found parallel - /usr/local/bin/parallel
[14:45:45] Found freebayes - /usr/local/bin/freebayes
[14:45:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:45] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:45] Found gzip - /bin/gzip
[14:45:45] Found vt - /usr/local/bin/vt
[14:45:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:46:03] This is snippy 4.6.0Show full stderr[14:46:03] This is snippy 4.6.0
[14:46:03] Written by Torsten Seemann
[14:46:03] Obtained from https://github.com/tseemann/snippy
[14:46:03] Detected operating system: linux
[14:46:03] Enabling bundled linux tools.
[14:46:03] Found bwa - /usr/local/bin/bwa
[14:46:03] Found bcftools - /usr/local/bin/bcftools
[14:46:03] Found samtools - /usr/local/bin/samtools
[14:46:04] Found java - /usr/local/bin/java
[14:46:04] Found snpEff - /usr/local/bin/snpEff
[14:46:04] Found samclip - /usr/local/bin/samclip
[14:46:04] Found seqtk - /usr/local/bin/seqtk
[14:46:04] Found parallel - /usr/local/bin/parallel
[14:46:04] Found freebayes - /usr/local/bin/freebayes
[14:46:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:04] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:04] Found gzip - /bin/gzip
[14:46:04] Found vt - /usr/local/bin/vt
[14:46:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:45:30] This is snippy 4.6.0Show full stderr[14:45:30] This is snippy 4.6.0
[14:45:30] Written by Torsten Seemann
[14:45:30] Obtained from https://github.com/tseemann/snippy
[14:45:30] Detected operating system: linux
[14:45:30] Enabling bundled linux tools.
[14:45:30] Found bwa - /usr/local/bin/bwa
[14:45:30] Found bcftools - /usr/local/bin/bcftools
[14:45:30] Found samtools - /usr/local/bin/samtools
[14:45:30] Found java - /usr/local/bin/java
[14:45:30] Found snpEff - /usr/local/bin/snpEff
[14:45:30] Found samclip - /usr/local/bin/samclip
[14:45:30] Found seqtk - /usr/local/bin/seqtk
[14:45:30] Found parallel - /usr/local/bin/parallel
[14:45:30] Found freebayes - /usr/local/bin/freebayes
[14:45:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:30] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:30] Found gzip - /bin/gzip
[14:45:30] Found vt - /usr/local/bin/vt
[14:45:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:45:33] This is snippy 4.6.0Show full stderr[14:45:33] This is snippy 4.6.0
[14:45:33] Written by Torsten Seemann
[14:45:33] Obtained from https://github.com/tseemann/snippy
[14:45:33] Detected operating system: linux
[14:45:33] Enabling bundled linux tools.
[14:45:33] Found bwa - /usr/local/bin/bwa
[14:45:33] Found bcftools - /usr/local/bin/bcftools
[14:45:33] Found samtools - /usr/local/bin/samtools
[14:45:33] Found java - /usr/local/bin/java
[14:45:33] Found snpEff - /usr/local/bin/snpEff
[14:45:33] Found samclip - /usr/local/bin/samclip
[14:45:33] Found seqtk - /usr/local/bin/seqtk
[14:45:33] Found parallel - /usr/local/bin/parallel
[14:45:33] Found freebayes - /usr/local/bin/freebayes
[14:45:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:33] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:33] Found gzip - /bin/gzip
[14:45:33] Found vt - /usr/local/bin/vt
[14:45:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:45:48] This is snippy 4.6.0Show full stderr[14:45:48] This is snippy 4.6.0
[14:45:48] Written by Torsten Seemann
[14:45:48] Obtained from https://github.com/tseemann/snippy
[14:45:48] Detected operating system: linux
[14:45:48] Enabling bundled linux tools.
[14:45:48] Found bwa - /usr/local/bin/bwa
[14:45:48] Found bcftools - /usr/local/bin/bcftools
[14:45:48] Found samtools - /usr/local/bin/samtools
[14:45:48] Found java - /usr/local/bin/java
[14:45:48] Found snpEff - /usr/local/bin/snpEff
[14:45:48] Found samclip - /usr/local/bin/samclip
[14:45:48] Found seqtk - /usr/local/bin/seqtk
[14:45:48] Found parallel - /usr/local/bin/parallel
[14:45:48] Found freebayes - /usr/local/bin/freebayes
[14:45:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:48] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:48] Found gzip - /bin/gzip
[14:45:48] Found vt - /usr/local/bin/vt
[14:45:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:45:54] This is snippy 4.6.0Show full stderr[14:45:54] This is snippy 4.6.0
[14:45:54] Written by Torsten Seemann
[14:45:54] Obtained from https://github.com/tseemann/snippy
[14:45:54] Detected operating system: linux
[14:45:54] Enabling bundled linux tools.
[14:45:54] Found bwa - /usr/local/bin/bwa
[14:45:54] Found bcftools - /usr/local/bin/bcftools
[14:45:54] Found samtools - /usr/local/bin/samtools
[14:45:54] Found java - /usr/local/bin/java
[14:45:54] Found snpEff - /usr/local/bin/snpEff
[14:45:54] Found samclip - /usr/local/bin/samclip
[14:45:54] Found seqtk - /usr/local/bin/seqtk
[14:45:54] Found parallel - /usr/local/bin/parallel
[14:45:54] Found freebayes - /usr/local/bin/freebayes
[14:45:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:54] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:54] Found gzip - /bin/gzip
[14:45:54] Found vt - /usr/local/bin/vt
[14:45:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:50:57] This is snippy 4.6.0Show full stderr[14:50:57] This is snippy 4.6.0
[14:50:57] Written by Torsten Seemann
[14:50:57] Obtained from https://github.com/tseemann/snippy
[14:50:57] Detected operating system: linux
[14:50:57] Enabling bundled linux tools.
[14:50:57] Found bwa - /usr/local/bin/bwa
[14:50:57] Found bcftools - /usr/local/bin/bcftools
[14:50:57] Found samtools - /usr/local/bin/samtools
[14:50:57] Found java - /usr/local/bin/java
[14:50:57] Found snpEff - /usr/local/bin/snpEff
[14:50:57] Found samclip - /usr/local/bin/samclip
[14:50:57] Found seqtk - /usr/local/bin/seqtk
[14:50:57] Found parallel - /usr/local/bin/parallel
[14:50:57] Found freebayes - /usr/local/bin/freebayes
[14:50:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:57] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:57] Found gzip - /bin/gzip
[14:50:57] Found vt - /usr/local/bin/vt
[14:50:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:44:57] This is snippy 4.6.0Show full stderr[14:44:57] This is snippy 4.6.0
[14:44:57] Written by Torsten Seemann
[14:44:57] Obtained from https://github.com/tseemann/snippy
[14:44:57] Detected operating system: linux
[14:44:57] Enabling bundled linux tools.
[14:44:57] Found bwa - /usr/local/bin/bwa
[14:44:57] Found bcftools - /usr/local/bin/bcftools
[14:44:57] Found samtools - /usr/local/bin/samtools
[14:44:57] Found java - /usr/local/bin/java
[14:44:57] Found snpEff - /usr/local/bin/snpEff
[14:44:57] Found samclip - /usr/local/bin/samclip
[14:44:57] Found seqtk - /usr/local/bin/seqtk
[14:44:57] Found parallel - /usr/local/bin/parallel
[14:44:57] Found freebayes - /usr/local/bin/freebayes
[14:44:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:44:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:44:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:44:57] Found vcfuniq - /usr/local/bin/vcfuniq
[14:44:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:44:57] Found gzip - /bin/gzip
[14:44:57] Found vt - /usr/local/bin/vt
[14:44:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:44:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:44:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:44:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:44:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:44:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:44:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:44:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:46:58] This is snippy 4.6.0Show full stderr[14:46:58] This is snippy 4.6.0
[14:46:58] Written by Torsten Seemann
[14:46:58] Obtained from https://github.com/tseemann/snippy
[14:46:58] Detected operating system: linux
[14:46:58] Enabling bundled linux tools.
[14:46:58] Found bwa - /usr/local/bin/bwa
[14:46:58] Found bcftools - /usr/local/bin/bcftools
[14:46:58] Found samtools - /usr/local/bin/samtools
[14:46:58] Found java - /usr/local/bin/java
[14:46:58] Found snpEff - /usr/local/bin/snpEff
[14:46:59] Found samclip - /usr/local/bin/samclip
[14:46:59] Found seqtk - /usr/local/bin/seqtk
[14:46:59] Found parallel - /usr/local/bin/parallel
[14:46:59] Found freebayes - /usr/local/bin/freebayes
[14:46:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:59] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:59] Found gzip - /bin/gzip
[14:46:59] Found vt - /usr/local/bin/vt
[14:46:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:47:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:47:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:47:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:57:56] This is snippy 4.6.0Show full stderr[14:57:56] This is snippy 4.6.0
[14:57:56] Written by Torsten Seemann
[14:57:56] Obtained from https://github.com/tseemann/snippy
[14:57:56] Detected operating system: linux
[14:57:56] Enabling bundled linux tools.
[14:57:56] Found bwa - /usr/local/bin/bwa
[14:57:56] Found bcftools - /usr/local/bin/bcftools
[14:57:56] Found samtools - /usr/local/bin/samtools
[14:57:56] Found java - /usr/local/bin/java
[14:57:56] Found snpEff - /usr/local/bin/snpEff
[14:57:56] Found samclip - /usr/local/bin/samclip
[14:57:56] Found seqtk - /usr/local/bin/seqtk
[14:57:56] Found parallel - /usr/local/bin/parallel
[14:57:56] Found freebayes - /usr/local/bin/freebayes
[14:57:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:57:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:57:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:57:56] Found vcfuniq - /usr/local/bin/vcfuniq
[14:57:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:57:56] Found gzip - /bin/gzip
[14:57:56] Found vt - /usr/local/bin/vt
[14:57:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:57:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:57:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:57:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:57:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:57:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:57:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:57:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [15:02:56] This is snippy 4.6.0Show full stderr[15:02:56] This is snippy 4.6.0
[15:02:56] Written by Torsten Seemann
[15:02:56] Obtained from https://github.com/tseemann/snippy
[15:02:56] Detected operating system: linux
[15:02:56] Enabling bundled linux tools.
[15:02:56] Found bwa - /usr/local/bin/bwa
[15:02:56] Found bcftools - /usr/local/bin/bcftools
[15:02:56] Found samtools - /usr/local/bin/samtools
[15:02:56] Found java - /usr/local/bin/java
[15:02:56] Found snpEff - /usr/local/bin/snpEff
[15:02:56] Found samclip - /usr/local/bin/samclip
[15:02:56] Found seqtk - /usr/local/bin/seqtk
[15:02:56] Found parallel - /usr/local/bin/parallel
[15:02:56] Found freebayes - /usr/local/bin/freebayes
[15:02:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:02:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:02:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:02:56] Found vcfuniq - /usr/local/bin/vcfuniq
[15:02:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:02:56] Found gzip - /bin/gzip
[15:02:56] Found vt - /usr/local/bin/vt
[15:02:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:02:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:02:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:02:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:02:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:02:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:02:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:02:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:46:57] This is snippy 4.6.0Show full stderr[14:46:57] This is snippy 4.6.0
[14:46:57] Written by Torsten Seemann
[14:46:57] Obtained from https://github.com/tseemann/snippy
[14:46:57] Detected operating system: linux
[14:46:57] Enabling bundled linux tools.
[14:46:57] Found bwa - /usr/local/bin/bwa
[14:46:57] Found bcftools - /usr/local/bin/bcftools
[14:46:57] Found samtools - /usr/local/bin/samtools
[14:46:57] Found java - /usr/local/bin/java
[14:46:57] Found snpEff - /usr/local/bin/snpEff
[14:46:57] Found samclip - /usr/local/bin/samclip
[14:46:57] Found seqtk - /usr/local/bin/seqtk
[14:46:57] Found parallel - /usr/local/bin/parallel
[14:46:57] Found freebayes - /usr/local/bin/freebayes
[14:46:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:58] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:58] Found gzip - /bin/gzip
[14:46:58] Found vt - /usr/local/bin/vt
[14:46:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [15:14:57] This is snippy 4.6.0Show full stderr[15:14:57] This is snippy 4.6.0
[15:14:57] Written by Torsten Seemann
[15:14:57] Obtained from https://github.com/tseemann/snippy
[15:14:57] Detected operating system: linux
[15:14:57] Enabling bundled linux tools.
[15:14:57] Found bwa - /usr/local/bin/bwa
[15:14:57] Found bcftools - /usr/local/bin/bcftools
[15:14:57] Found samtools - /usr/local/bin/samtools
[15:14:57] Found java - /usr/local/bin/java
[15:14:57] Found snpEff - /usr/local/bin/snpEff
[15:14:57] Found samclip - /usr/local/bin/samclip
[15:14:57] Found seqtk - /usr/local/bin/seqtk
[15:14:57] Found parallel - /usr/local/bin/parallel
[15:14:57] Found freebayes - /usr/local/bin/freebayes
[15:14:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:14:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:14:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:14:57] Found vcfuniq - /usr/local/bin/vcfuniq
[15:14:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:14:57] Found gzip - /bin/gzip
[15:14:57] Found vt - /usr/local/bin/vt
[15:14:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:14:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:14:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:14:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:14:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:14:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:14:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:14:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:46:18] This is snippy 4.6.0Show full stderr[14:46:18] This is snippy 4.6.0
[14:46:18] Written by Torsten Seemann
[14:46:18] Obtained from https://github.com/tseemann/snippy
[14:46:18] Detected operating system: linux
[14:46:18] Enabling bundled linux tools.
[14:46:18] Found bwa - /usr/local/bin/bwa
[14:46:18] Found bcftools - /usr/local/bin/bcftools
[14:46:18] Found samtools - /usr/local/bin/samtools
[14:46:18] Found java - /usr/local/bin/java
[14:46:18] Found snpEff - /usr/local/bin/snpEff
[14:46:18] Found samclip - /usr/local/bin/samclip
[14:46:18] Found seqtk - /usr/local/bin/seqtk
[14:46:18] Found parallel - /usr/local/bin/parallel
[14:46:18] Found freebayes - /usr/local/bin/freebayes
[14:46:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:18] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:18] Found gzip - /bin/gzip
[14:46:18] Found vt - /usr/local/bin/vt
[14:46:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:48:42] This is snippy 4.6.0Show full stderr[14:48:42] This is snippy 4.6.0
[14:48:42] Written by Torsten Seemann
[14:48:42] Obtained from https://github.com/tseemann/snippy
[14:48:42] Detected operating system: linux
[14:48:42] Enabling bundled linux tools.
[14:48:42] Found bwa - /usr/local/bin/bwa
[14:48:42] Found bcftools - /usr/local/bin/bcftools
[14:48:42] Found samtools - /usr/local/bin/samtools
[14:48:42] Found java - /usr/local/bin/java
[14:48:42] Found snpEff - /usr/local/bin/snpEff
[14:48:42] Found samclip - /usr/local/bin/samclip
[14:48:42] Found seqtk - /usr/local/bin/seqtk
[14:48:42] Found parallel - /usr/local/bin/parallel
[14:48:42] Found freebayes - /usr/local/bin/freebayes
[14:48:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:42] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:42] Found gzip - /bin/gzip
[14:48:42] Found vt - /usr/local/bin/vt
[14:48:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:48:03] This is snippy 4.6.0Show full stderr[14:48:03] This is snippy 4.6.0
[14:48:03] Written by Torsten Seemann
[14:48:03] Obtained from https://github.com/tseemann/snippy
[14:48:03] Detected operating system: linux
[14:48:03] Enabling bundled linux tools.
[14:48:03] Found bwa - /usr/local/bin/bwa
[14:48:03] Found bcftools - /usr/local/bin/bcftools
[14:48:03] Found samtools - /usr/local/bin/samtools
[14:48:03] Found java - /usr/local/bin/java
[14:48:03] Found snpEff - /usr/local/bin/snpEff
[14:48:03] Found samclip - /usr/local/bin/samclip
[14:48:03] Found seqtk - /usr/local/bin/seqtk
[14:48:03] Found parallel - /usr/local/bin/parallel
[14:48:03] Found freebayes - /usr/local/bin/freebayes
[14:48:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:03] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:03] Found gzip - /bin/gzip
[14:48:03] Found vt - /usr/local/bin/vt
[14:48:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:47:51] This is snippy 4.6.0Show full stderr[14:47:51] This is snippy 4.6.0
[14:47:51] Written by Torsten Seemann
[14:47:51] Obtained from https://github.com/tseemann/snippy
[14:47:51] Detected operating system: linux
[14:47:51] Enabling bundled linux tools.
[14:47:51] Found bwa - /usr/local/bin/bwa
[14:47:51] Found bcftools - /usr/local/bin/bcftools
[14:47:51] Found samtools - /usr/local/bin/samtools
[14:47:51] Found java - /usr/local/bin/java
[14:47:51] Found snpEff - /usr/local/bin/snpEff
[14:47:51] Found samclip - /usr/local/bin/samclip
[14:47:51] Found seqtk - /usr/local/bin/seqtk
[14:47:51] Found parallel - /usr/local/bin/parallel
[14:47:51] Found freebayes - /usr/local/bin/freebayes
[14:47:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:47:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:47:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:47:51] Found vcfuniq - /usr/local/bin/vcfuniq
[14:47:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:47:51] Found gzip - /bin/gzip
[14:47:51] Found vt - /usr/local/bin/vt
[14:47:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:47:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:47:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:47:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:47:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:47:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:47:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:47:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:48:57] This is snippy 4.6.0Show full stderr[14:48:57] This is snippy 4.6.0
[14:48:57] Written by Torsten Seemann
[14:48:57] Obtained from https://github.com/tseemann/snippy
[14:48:57] Detected operating system: linux
[14:48:57] Enabling bundled linux tools.
[14:48:57] Found bwa - /usr/local/bin/bwa
[14:48:57] Found bcftools - /usr/local/bin/bcftools
[14:48:57] Found samtools - /usr/local/bin/samtools
[14:48:57] Found java - /usr/local/bin/java
[14:48:57] Found snpEff - /usr/local/bin/snpEff
[14:48:57] Found samclip - /usr/local/bin/samclip
[14:48:57] Found seqtk - /usr/local/bin/seqtk
[14:48:57] Found parallel - /usr/local/bin/parallel
[14:48:57] Found freebayes - /usr/local/bin/freebayes
[14:48:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:57] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:57] Found gzip - /bin/gzip
[14:48:57] Found vt - /usr/local/bin/vt
[14:48:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:49:26] This is snippy 4.6.0Show full stderr[14:49:26] This is snippy 4.6.0
[14:49:26] Written by Torsten Seemann
[14:49:26] Obtained from https://github.com/tseemann/snippy
[14:49:26] Detected operating system: linux
[14:49:26] Enabling bundled linux tools.
[14:49:26] Found bwa - /usr/local/bin/bwa
[14:49:26] Found bcftools - /usr/local/bin/bcftools
[14:49:26] Found samtools - /usr/local/bin/samtools
[14:49:26] Found java - /usr/local/bin/java
[14:49:26] Found snpEff - /usr/local/bin/snpEff
[14:49:26] Found samclip - /usr/local/bin/samclip
[14:49:26] Found seqtk - /usr/local/bin/seqtk
[14:49:26] Found parallel - /usr/local/bin/parallel
[14:49:26] Found freebayes - /usr/local/bin/freebayes
[14:49:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:26] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:26] Found gzip - /bin/gzip
[14:49:26] Found vt - /usr/local/bin/vt
[14:49:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:49:11] This is snippy 4.6.0Show full stderr[14:49:11] This is snippy 4.6.0
[14:49:11] Written by Torsten Seemann
[14:49:11] Obtained from https://github.com/tseemann/snippy
[14:49:11] Detected operating system: linux
[14:49:11] Enabling bundled linux tools.
[14:49:11] Found bwa - /usr/local/bin/bwa
[14:49:11] Found bcftools - /usr/local/bin/bcftools
[14:49:11] Found samtools - /usr/local/bin/samtools
[14:49:11] Found java - /usr/local/bin/java
[14:49:11] Found snpEff - /usr/local/bin/snpEff
[14:49:11] Found samclip - /usr/local/bin/samclip
[14:49:11] Found seqtk - /usr/local/bin/seqtk
[14:49:11] Found parallel - /usr/local/bin/parallel
[14:49:11] Found freebayes - /usr/local/bin/freebayes
[14:49:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:11] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:11] Found gzip - /bin/gzip
[14:49:11] Found vt - /usr/local/bin/vt
[14:49:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:49:40] This is snippy 4.6.0Show full stderr[14:49:40] This is snippy 4.6.0
[14:49:40] Written by Torsten Seemann
[14:49:40] Obtained from https://github.com/tseemann/snippy
[14:49:40] Detected operating system: linux
[14:49:40] Enabling bundled linux tools.
[14:49:40] Found bwa - /usr/local/bin/bwa
[14:49:40] Found bcftools - /usr/local/bin/bcftools
[14:49:40] Found samtools - /usr/local/bin/samtools
[14:49:40] Found java - /usr/local/bin/java
[14:49:40] Found snpEff - /usr/local/bin/snpEff
[14:49:40] Found samclip - /usr/local/bin/samclip
[14:49:40] Found seqtk - /usr/local/bin/seqtk
[14:49:40] Found parallel - /usr/local/bin/parallel
[14:49:40] Found freebayes - /usr/local/bin/freebayes
[14:49:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:40] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:40] Found gzip - /bin/gzip
[14:49:40] Found vt - /usr/local/bin/vt
[14:49:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:49:58] This is snippy 4.6.0Show full stderr[14:49:58] This is snippy 4.6.0
[14:49:58] Written by Torsten Seemann
[14:49:58] Obtained from https://github.com/tseemann/snippy
[14:49:58] Detected operating system: linux
[14:49:58] Enabling bundled linux tools.
[14:49:58] Found bwa - /usr/local/bin/bwa
[14:49:58] Found bcftools - /usr/local/bin/bcftools
[14:49:58] Found samtools - /usr/local/bin/samtools
[14:49:58] Found java - /usr/local/bin/java
[14:49:58] Found snpEff - /usr/local/bin/snpEff
[14:49:58] Found samclip - /usr/local/bin/samclip
[14:49:58] Found seqtk - /usr/local/bin/seqtk
[14:49:58] Found parallel - /usr/local/bin/parallel
[14:49:58] Found freebayes - /usr/local/bin/freebayes
[14:49:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:58] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:58] Found gzip - /bin/gzip
[14:49:58] Found vt - /usr/local/bin/vt
[14:49:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:51:37] This is snippy 4.6.0Show full stderr[14:51:37] This is snippy 4.6.0
[14:51:37] Written by Torsten Seemann
[14:51:37] Obtained from https://github.com/tseemann/snippy
[14:51:37] Detected operating system: linux
[14:51:37] Enabling bundled linux tools.
[14:51:37] Found bwa - /usr/local/bin/bwa
[14:51:37] Found bcftools - /usr/local/bin/bcftools
[14:51:37] Found samtools - /usr/local/bin/samtools
[14:51:37] Found java - /usr/local/bin/java
[14:51:37] Found snpEff - /usr/local/bin/snpEff
[14:51:37] Found samclip - /usr/local/bin/samclip
[14:51:37] Found seqtk - /usr/local/bin/seqtk
[14:51:37] Found parallel - /usr/local/bin/parallel
[14:51:37] Found freebayes - /usr/local/bin/freebayes
[14:51:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:37] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:37] Found gzip - /bin/gzip
[14:51:37] Found vt - /usr/local/bin/vt
[14:51:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:52:23] This is snippy 4.6.0Show full stderr[14:52:23] This is snippy 4.6.0
[14:52:23] Written by Torsten Seemann
[14:52:23] Obtained from https://github.com/tseemann/snippy
[14:52:23] Detected operating system: linux
[14:52:23] Enabling bundled linux tools.
[14:52:23] Found bwa - /usr/local/bin/bwa
[14:52:23] Found bcftools - /usr/local/bin/bcftools
[14:52:23] Found samtools - /usr/local/bin/samtools
[14:52:23] Found java - /usr/local/bin/java
[14:52:23] Found snpEff - /usr/local/bin/snpEff
[14:52:23] Found samclip - /usr/local/bin/samclip
[14:52:23] Found seqtk - /usr/local/bin/seqtk
[14:52:23] Found parallel - /usr/local/bin/parallel
[14:52:23] Found freebayes - /usr/local/bin/freebayes
[14:52:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:52:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:52:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:52:23] Found vcfuniq - /usr/local/bin/vcfuniq
[14:52:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:52:23] Found gzip - /bin/gzip
[14:52:23] Found vt - /usr/local/bin/vt
[14:52:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:52:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:52:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:52:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:52:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:52:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:52:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:52:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:52:35] This is snippy 4.6.0Show full stderr[14:52:35] This is snippy 4.6.0
[14:52:35] Written by Torsten Seemann
[14:52:35] Obtained from https://github.com/tseemann/snippy
[14:52:35] Detected operating system: linux
[14:52:35] Enabling bundled linux tools.
[14:52:35] Found bwa - /usr/local/bin/bwa
[14:52:35] Found bcftools - /usr/local/bin/bcftools
[14:52:35] Found samtools - /usr/local/bin/samtools
[14:52:35] Found java - /usr/local/bin/java
[14:52:35] Found snpEff - /usr/local/bin/snpEff
[14:52:35] Found samclip - /usr/local/bin/samclip
[14:52:35] Found seqtk - /usr/local/bin/seqtk
[14:52:35] Found parallel - /usr/local/bin/parallel
[14:52:35] Found freebayes - /usr/local/bin/freebayes
[14:52:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:52:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:52:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:52:35] Found vcfuniq - /usr/local/bin/vcfuniq
[14:52:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:52:35] Found gzip - /bin/gzip
[14:52:35] Found vt - /usr/local/bin/vt
[14:52:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:52:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:52:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:52:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:52:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:52:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:52:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:52:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:50:59] This is snippy 4.6.0Show full stderr[14:50:59] This is snippy 4.6.0
[14:50:59] Written by Torsten Seemann
[14:50:59] Obtained from https://github.com/tseemann/snippy
[14:50:59] Detected operating system: linux
[14:50:59] Enabling bundled linux tools.
[14:50:59] Found bwa - /usr/local/bin/bwa
[14:50:59] Found bcftools - /usr/local/bin/bcftools
[14:50:59] Found samtools - /usr/local/bin/samtools
[14:50:59] Found java - /usr/local/bin/java
[14:50:59] Found snpEff - /usr/local/bin/snpEff
[14:50:59] Found samclip - /usr/local/bin/samclip
[14:50:59] Found seqtk - /usr/local/bin/seqtk
[14:50:59] Found parallel - /usr/local/bin/parallel
[14:50:59] Found freebayes - /usr/local/bin/freebayes
[14:50:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:00] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:00] Found gzip - /bin/gzip
[14:51:00] Found vt - /usr/local/bin/vt
[14:51:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:51:23] This is snippy 4.6.0Show full stderr[14:51:23] This is snippy 4.6.0
[14:51:23] Written by Torsten Seemann
[14:51:23] Obtained from https://github.com/tseemann/snippy
[14:51:23] Detected operating system: linux
[14:51:23] Enabling bundled linux tools.
[14:51:23] Found bwa - /usr/local/bin/bwa
[14:51:23] Found bcftools - /usr/local/bin/bcftools
[14:51:23] Found samtools - /usr/local/bin/samtools
[14:51:23] Found java - /usr/local/bin/java
[14:51:23] Found snpEff - /usr/local/bin/snpEff
[14:51:23] Found samclip - /usr/local/bin/samclip
[14:51:23] Found seqtk - /usr/local/bin/seqtk
[14:51:23] Found parallel - /usr/local/bin/parallel
[14:51:23] Found freebayes - /usr/local/bin/freebayes
[14:51:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:23] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:23] Found gzip - /bin/gzip
[14:51:23] Found vt - /usr/local/bin/vt
[14:51:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:52:08] This is snippy 4.6.0Show full stderr[14:52:08] This is snippy 4.6.0
[14:52:08] Written by Torsten Seemann
[14:52:08] Obtained from https://github.com/tseemann/snippy
[14:52:08] Detected operating system: linux
[14:52:08] Enabling bundled linux tools.
[14:52:08] Found bwa - /usr/local/bin/bwa
[14:52:08] Found bcftools - /usr/local/bin/bcftools
[14:52:08] Found samtools - /usr/local/bin/samtools
[14:52:08] Found java - /usr/local/bin/java
[14:52:08] Found snpEff - /usr/local/bin/snpEff
[14:52:08] Found samclip - /usr/local/bin/samclip
[14:52:08] Found seqtk - /usr/local/bin/seqtk
[14:52:08] Found parallel - /usr/local/bin/parallel
[14:52:08] Found freebayes - /usr/local/bin/freebayes
[14:52:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:52:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:52:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:52:08] Found vcfuniq - /usr/local/bin/vcfuniq
[14:52:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:52:08] Found gzip - /bin/gzip
[14:52:08] Found vt - /usr/local/bin/vt
[14:52:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:52:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:52:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:52:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:52:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:52:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:52:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:52:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:49:44] This is snippy 4.6.0Show full stderr[14:49:44] This is snippy 4.6.0
[14:49:44] Written by Torsten Seemann
[14:49:44] Obtained from https://github.com/tseemann/snippy
[14:49:44] Detected operating system: linux
[14:49:44] Enabling bundled linux tools.
[14:49:44] Found bwa - /usr/local/bin/bwa
[14:49:44] Found bcftools - /usr/local/bin/bcftools
[14:49:44] Found samtools - /usr/local/bin/samtools
[14:49:44] Found java - /usr/local/bin/java
[14:49:44] Found snpEff - /usr/local/bin/snpEff
[14:49:44] Found samclip - /usr/local/bin/samclip
[14:49:44] Found seqtk - /usr/local/bin/seqtk
[14:49:44] Found parallel - /usr/local/bin/parallel
[14:49:44] Found freebayes - /usr/local/bin/freebayes
[14:49:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:44] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:44] Found gzip - /bin/gzip
[14:49:44] Found vt - /usr/local/bin/vt
[14:49:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:51:57] This is snippy 4.6.0Show full stderr[14:51:57] This is snippy 4.6.0
[14:51:57] Written by Torsten Seemann
[14:51:57] Obtained from https://github.com/tseemann/snippy
[14:51:57] Detected operating system: linux
[14:51:57] Enabling bundled linux tools.
[14:51:57] Found bwa - /usr/local/bin/bwa
[14:51:57] Found bcftools - /usr/local/bin/bcftools
[14:51:57] Found samtools - /usr/local/bin/samtools
[14:51:57] Found java - /usr/local/bin/java
[14:51:57] Found snpEff - /usr/local/bin/snpEff
[14:51:57] Found samclip - /usr/local/bin/samclip
[14:51:57] Found seqtk - /usr/local/bin/seqtk
[14:51:57] Found parallel - /usr/local/bin/parallel
[14:51:57] Found freebayes - /usr/local/bin/freebayes
[14:51:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:57] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:57] Found gzip - /bin/gzip
[14:51:57] Found vt - /usr/local/bin/vt
[14:51:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:53:07] This is snippy 4.6.0Show full stderr[14:53:07] This is snippy 4.6.0
[14:53:07] Written by Torsten Seemann
[14:53:07] Obtained from https://github.com/tseemann/snippy
[14:53:07] Detected operating system: linux
[14:53:07] Enabling bundled linux tools.
[14:53:07] Found bwa - /usr/local/bin/bwa
[14:53:07] Found bcftools - /usr/local/bin/bcftools
[14:53:07] Found samtools - /usr/local/bin/samtools
[14:53:07] Found java - /usr/local/bin/java
[14:53:07] Found snpEff - /usr/local/bin/snpEff
[14:53:07] Found samclip - /usr/local/bin/samclip
[14:53:07] Found seqtk - /usr/local/bin/seqtk
[14:53:07] Found parallel - /usr/local/bin/parallel
[14:53:07] Found freebayes - /usr/local/bin/freebayes
[14:53:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:53:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:53:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:53:07] Found vcfuniq - /usr/local/bin/vcfuniq
[14:53:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:53:07] Found gzip - /bin/gzip
[14:53:07] Found vt - /usr/local/bin/vt
[14:53:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:53:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:53:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:53:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:53:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:53:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:53:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:53:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:53:19] This is snippy 4.6.0Show full stderr[14:53:19] This is snippy 4.6.0
[14:53:19] Written by Torsten Seemann
[14:53:19] Obtained from https://github.com/tseemann/snippy
[14:53:19] Detected operating system: linux
[14:53:19] Enabling bundled linux tools.
[14:53:19] Found bwa - /usr/local/bin/bwa
[14:53:19] Found bcftools - /usr/local/bin/bcftools
[14:53:19] Found samtools - /usr/local/bin/samtools
[14:53:19] Found java - /usr/local/bin/java
[14:53:19] Found snpEff - /usr/local/bin/snpEff
[14:53:19] Found samclip - /usr/local/bin/samclip
[14:53:19] Found seqtk - /usr/local/bin/seqtk
[14:53:19] Found parallel - /usr/local/bin/parallel
[14:53:19] Found freebayes - /usr/local/bin/freebayes
[14:53:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:53:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:53:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:53:19] Found vcfuniq - /usr/local/bin/vcfuniq
[14:53:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:53:19] Found gzip - /bin/gzip
[14:53:19] Found vt - /usr/local/bin/vt
[14:53:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:53:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:53:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:53:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:53:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:53:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:53:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:53:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:53:22] This is snippy 4.6.0Show full stderr[14:53:22] This is snippy 4.6.0
[14:53:22] Written by Torsten Seemann
[14:53:22] Obtained from https://github.com/tseemann/snippy
[14:53:22] Detected operating system: linux
[14:53:22] Enabling bundled linux tools.
[14:53:22] Found bwa - /usr/local/bin/bwa
[14:53:22] Found bcftools - /usr/local/bin/bcftools
[14:53:22] Found samtools - /usr/local/bin/samtools
[14:53:22] Found java - /usr/local/bin/java
[14:53:22] Found snpEff - /usr/local/bin/snpEff
[14:53:22] Found samclip - /usr/local/bin/samclip
[14:53:22] Found seqtk - /usr/local/bin/seqtk
[14:53:22] Found parallel - /usr/local/bin/parallel
[14:53:22] Found freebayes - /usr/local/bin/freebayes
[14:53:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:53:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:53:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:53:22] Found vcfuniq - /usr/local/bin/vcfuniq
[14:53:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:53:22] Found gzip - /bin/gzip
[14:53:22] Found vt - /usr/local/bin/vt
[14:53:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:53:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:53:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:53:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:53:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:53:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:53:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:53:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:53:33] This is snippy 4.6.0Show full stderr[14:53:33] This is snippy 4.6.0
[14:53:33] Written by Torsten Seemann
[14:53:33] Obtained from https://github.com/tseemann/snippy
[14:53:33] Detected operating system: linux
[14:53:33] Enabling bundled linux tools.
[14:53:33] Found bwa - /usr/local/bin/bwa
[14:53:33] Found bcftools - /usr/local/bin/bcftools
[14:53:33] Found samtools - /usr/local/bin/samtools
[14:53:33] Found java - /usr/local/bin/java
[14:53:33] Found snpEff - /usr/local/bin/snpEff
[14:53:33] Found samclip - /usr/local/bin/samclip
[14:53:33] Found seqtk - /usr/local/bin/seqtk
[14:53:33] Found parallel - /usr/local/bin/parallel
[14:53:33] Found freebayes - /usr/local/bin/freebayes
[14:53:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:53:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:53:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:53:33] Found vcfuniq - /usr/local/bin/vcfuniq
[14:53:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:53:33] Found gzip - /bin/gzip
[14:53:33] Found vt - /usr/local/bin/vt
[14:53:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:53:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:53:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:53:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:53:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:53:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:53:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:53:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:53:36] This is snippy 4.6.0Show full stderr[14:53:36] This is snippy 4.6.0
[14:53:36] Written by Torsten Seemann
[14:53:36] Obtained from https://github.com/tseemann/snippy
[14:53:36] Detected operating system: linux
[14:53:36] Enabling bundled linux tools.
[14:53:36] Found bwa - /usr/local/bin/bwa
[14:53:36] Found bcftools - /usr/local/bin/bcftools
[14:53:36] Found samtools - /usr/local/bin/samtools
[14:53:36] Found java - /usr/local/bin/java
[14:53:36] Found snpEff - /usr/local/bin/snpEff
[14:53:36] Found samclip - /usr/local/bin/samclip
[14:53:36] Found seqtk - /usr/local/bin/seqtk
[14:53:36] Found parallel - /usr/local/bin/parallel
[14:53:36] Found freebayes - /usr/local/bin/freebayes
[14:53:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:53:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:53:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:53:36] Found vcfuniq - /usr/local/bin/vcfuniq
[14:53:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:53:36] Found gzip - /bin/gzip
[14:53:36] Found vt - /usr/local/bin/vt
[14:53:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:53:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:53:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:53:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:53:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:53:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:53:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:53:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [14:53:47] This is snippy 4.6.0Show full stderr[14:53:47] This is snippy 4.6.0
[14:53:47] Written by Torsten Seemann
[14:53:47] Obtained from https://github.com/tseemann/snippy
[14:53:47] Detected operating system: linux
[14:53:47] Enabling bundled linux tools.
[14:53:47] Found bwa - /usr/local/bin/bwa
[14:53:47] Found bcftools - /usr/local/bin/bcftools
[14:53:47] Found samtools - /usr/local/bin/samtools
[14:53:47] Found java - /usr/local/bin/java
[14:53:47] Found snpEff - /usr/local/bin/snpEff
[14:53:47] Found samclip - /usr/local/bin/samclip
[14:53:47] Found seqtk - /usr/local/bin/seqtk
[14:53:47] Found parallel - /usr/local/bin/parallel
[14:53:47] Found freebayes - /usr/local/bin/freebayes
[14:53:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:53:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:53:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:53:47] Found vcfuniq - /usr/local/bin/vcfuniq
[14:53:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:53:47] Found gzip - /bin/gzip
[14:53:47] Found vt - /usr/local/bin/vt
[14:53:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:53:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:53:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:53:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:53:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:53:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:53:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:53:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [16:04:43] This is snippy 4.6.0Show full stderr[16:04:43] This is snippy 4.6.0
[16:04:43] Written by Torsten Seemann
[16:04:43] Obtained from https://github.com/tseemann/snippy
[16:04:43] Detected operating system: linux
[16:04:43] Enabling bundled linux tools.
[16:04:43] Found bwa - /usr/local/bin/bwa
[16:04:43] Found bcftools - /usr/local/bin/bcftools
[16:04:43] Found samtools - /usr/local/bin/samtools
[16:04:43] Found java - /usr/local/bin/java
[16:04:43] Found snpEff - /usr/local/bin/snpEff
[16:04:43] Found samclip - /usr/local/bin/samclip
[16:04:43] Found seqtk - /usr/local/bin/seqtk
[16:04:43] Found parallel - /usr/local/bin/parallel
[16:04:43] Found freebayes - /usr/local/bin/freebayes
[16:04:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:04:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:04:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:04:43] Found vcfuniq - /usr/local/bin/vcfuniq
[16:04:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:04:43] Found gzip - /bin/gzip
[16:04:43] Found vt - /usr/local/bin/vt
[16:04:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:04:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:04:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:04:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:04:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:04:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:04:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:04:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:08:15] This is snippy 4.6.0Show full stderr[17:08:15] This is snippy 4.6.0
[17:08:15] Written by Torsten Seemann
[17:08:15] Obtained from https://github.com/tseemann/snippy
[17:08:15] Detected operating system: linux
[17:08:15] Enabling bundled linux tools.
[17:08:15] Found bwa - /usr/local/bin/bwa
[17:08:15] Found bcftools - /usr/local/bin/bcftools
[17:08:15] Found samtools - /usr/local/bin/samtools
[17:08:15] Found java - /usr/local/bin/java
[17:08:15] Found snpEff - /usr/local/bin/snpEff
[17:08:15] Found samclip - /usr/local/bin/samclip
[17:08:15] Found seqtk - /usr/local/bin/seqtk
[17:08:15] Found parallel - /usr/local/bin/parallel
[17:08:15] Found freebayes - /usr/local/bin/freebayes
[17:08:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:08:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:08:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:08:15] Found vcfuniq - /usr/local/bin/vcfuniq
[17:08:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:08:15] Found gzip - /bin/gzip
[17:08:15] Found vt - /usr/local/bin/vt
[17:08:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:08:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:08:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:08:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:08:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:08:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:08:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:08:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [19:07:30] This is snippy 4.6.0Show full stderr[19:07:30] This is snippy 4.6.0
[19:07:30] Written by Torsten Seemann
[19:07:30] Obtained from https://github.com/tseemann/snippy
[19:07:30] Detected operating system: linux
[19:07:30] Enabling bundled linux tools.
[19:07:30] Found bwa - /usr/local/bin/bwa
[19:07:30] Found bcftools - /usr/local/bin/bcftools
[19:07:30] Found samtools - /usr/local/bin/samtools
[19:07:30] Found java - /usr/local/bin/java
[19:07:30] Found snpEff - /usr/local/bin/snpEff
[19:07:30] Found samclip - /usr/local/bin/samclip
[19:07:30] Found seqtk - /usr/local/bin/seqtk
[19:07:30] Found parallel - /usr/local/bin/parallel
[19:07:30] Found freebayes - /usr/local/bin/freebayes
[19:07:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:07:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:07:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:07:30] Found vcfuniq - /usr/local/bin/vcfuniq
[19:07:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:07:30] Found gzip - /bin/gzip
[19:07:30] Found vt - /usr/local/bin/vt
[19:07:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:07:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:07:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:07:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:07:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:07:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:07:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:07:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [19:24:15] This is snippy 4.6.0Show full stderr[19:24:15] This is snippy 4.6.0
[19:24:15] Written by Torsten Seemann
[19:24:15] Obtained from https://github.com/tseemann/snippy
[19:24:15] Detected operating system: linux
[19:24:15] Enabling bundled linux tools.
[19:24:15] Found bwa - /usr/local/bin/bwa
[19:24:15] Found bcftools - /usr/local/bin/bcftools
[19:24:15] Found samtools - /usr/local/bin/samtools
[19:24:15] Found java - /usr/local/bin/java
[19:24:15] Found snpEff - /usr/local/bin/snpEff
[19:24:15] Found samclip - /usr/local/bin/samclip
[19:24:15] Found seqtk - /usr/local/bin/seqtk
[19:24:15] Found parallel - /usr/local/bin/parallel
[19:24:15] Found freebayes - /usr/local/bin/freebayes
[19:24:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:24:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:24:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:24:15] Found vcfuniq - /usr/local/bin/vcfuniq
[19:24:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:24:15] Found gzip - /bin/gzip
[19:24:15] Found vt - /usr/local/bin/vt
[19:24:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:24:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:24:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:24:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:24:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:24:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:24:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:24:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:08:31] This is snippy 4.6.0Show full stderr[17:08:31] This is snippy 4.6.0
[17:08:31] Written by Torsten Seemann
[17:08:31] Obtained from https://github.com/tseemann/snippy
[17:08:31] Detected operating system: linux
[17:08:31] Enabling bundled linux tools.
[17:08:31] Found bwa - /usr/local/bin/bwa
[17:08:31] Found bcftools - /usr/local/bin/bcftools
[17:08:31] Found samtools - /usr/local/bin/samtools
[17:08:31] Found java - /usr/local/bin/java
[17:08:31] Found snpEff - /usr/local/bin/snpEff
[17:08:31] Found samclip - /usr/local/bin/samclip
[17:08:31] Found seqtk - /usr/local/bin/seqtk
[17:08:31] Found parallel - /usr/local/bin/parallel
[17:08:31] Found freebayes - /usr/local/bin/freebayes
[17:08:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:08:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:08:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:08:31] Found vcfuniq - /usr/local/bin/vcfuniq
[17:08:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:08:31] Found gzip - /bin/gzip
[17:08:31] Found vt - /usr/local/bin/vt
[17:08:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:08:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:08:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:08:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:08:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:08:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:08:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:08:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [20:14:00] This is snippy 4.6.0Show full stderr[20:14:00] This is snippy 4.6.0
[20:14:00] Written by Torsten Seemann
[20:14:00] Obtained from https://github.com/tseemann/snippy
[20:14:00] Detected operating system: linux
[20:14:00] Enabling bundled linux tools.
[20:14:00] Found bwa - /usr/local/bin/bwa
[20:14:00] Found bcftools - /usr/local/bin/bcftools
[20:14:00] Found samtools - /usr/local/bin/samtools
[20:14:00] Found java - /usr/local/bin/java
[20:14:00] Found snpEff - /usr/local/bin/snpEff
[20:14:00] Found samclip - /usr/local/bin/samclip
[20:14:00] Found seqtk - /usr/local/bin/seqtk
[20:14:00] Found parallel - /usr/local/bin/parallel
[20:14:00] Found freebayes - /usr/local/bin/freebayes
[20:14:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:14:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:14:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:14:00] Found vcfuniq - /usr/local/bin/vcfuniq
[20:14:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:14:00] Found gzip - /bin/gzip
[20:14:00] Found vt - /usr/local/bin/vt
[20:14:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:14:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:14:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:14:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:14:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:14:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:14:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:14:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [18:09:47] This is snippy 4.6.0Show full stderr[18:09:47] This is snippy 4.6.0
[18:09:47] Written by Torsten Seemann
[18:09:47] Obtained from https://github.com/tseemann/snippy
[18:09:47] Detected operating system: linux
[18:09:47] Enabling bundled linux tools.
[18:09:47] Found bwa - /usr/local/bin/bwa
[18:09:47] Found bcftools - /usr/local/bin/bcftools
[18:09:47] Found samtools - /usr/local/bin/samtools
[18:09:47] Found java - /usr/local/bin/java
[18:09:47] Found snpEff - /usr/local/bin/snpEff
[18:09:47] Found samclip - /usr/local/bin/samclip
[18:09:47] Found seqtk - /usr/local/bin/seqtk
[18:09:47] Found parallel - /usr/local/bin/parallel
[18:09:47] Found freebayes - /usr/local/bin/freebayes
[18:09:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:09:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:09:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:09:47] Found vcfuniq - /usr/local/bin/vcfuniq
[18:09:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:09:47] Found gzip - /bin/gzip
[18:09:47] Found vt - /usr/local/bin/vt
[18:09:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:09:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:09:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:09:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:09:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:09:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:09:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:09:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:25:46] This is snippy 4.6.0Show full stderr[17:25:46] This is snippy 4.6.0
[17:25:46] Written by Torsten Seemann
[17:25:46] Obtained from https://github.com/tseemann/snippy
[17:25:46] Detected operating system: linux
[17:25:46] Enabling bundled linux tools.
[17:25:46] Found bwa - /usr/local/bin/bwa
[17:25:46] Found bcftools - /usr/local/bin/bcftools
[17:25:46] Found samtools - /usr/local/bin/samtools
[17:25:46] Found java - /usr/local/bin/java
[17:25:46] Found snpEff - /usr/local/bin/snpEff
[17:25:46] Found samclip - /usr/local/bin/samclip
[17:25:46] Found seqtk - /usr/local/bin/seqtk
[17:25:46] Found parallel - /usr/local/bin/parallel
[17:25:46] Found freebayes - /usr/local/bin/freebayes
[17:25:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:46] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:46] Found gzip - /bin/gzip
[17:25:46] Found vt - /usr/local/bin/vt
[17:25:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:25:31] This is snippy 4.6.0Show full stderr[17:25:31] This is snippy 4.6.0
[17:25:31] Written by Torsten Seemann
[17:25:31] Obtained from https://github.com/tseemann/snippy
[17:25:31] Detected operating system: linux
[17:25:31] Enabling bundled linux tools.
[17:25:31] Found bwa - /usr/local/bin/bwa
[17:25:31] Found bcftools - /usr/local/bin/bcftools
[17:25:31] Found samtools - /usr/local/bin/samtools
[17:25:31] Found java - /usr/local/bin/java
[17:25:31] Found snpEff - /usr/local/bin/snpEff
[17:25:31] Found samclip - /usr/local/bin/samclip
[17:25:31] Found seqtk - /usr/local/bin/seqtk
[17:25:31] Found parallel - /usr/local/bin/parallel
[17:25:31] Found freebayes - /usr/local/bin/freebayes
[17:25:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:31] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:31] Found gzip - /bin/gzip
[17:25:31] Found vt - /usr/local/bin/vt
[17:25:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [20:47:17] This is snippy 4.6.0Show full stderr[20:47:17] This is snippy 4.6.0
[20:47:17] Written by Torsten Seemann
[20:47:17] Obtained from https://github.com/tseemann/snippy
[20:47:17] Detected operating system: linux
[20:47:17] Enabling bundled linux tools.
[20:47:17] Found bwa - /usr/local/bin/bwa
[20:47:17] Found bcftools - /usr/local/bin/bcftools
[20:47:17] Found samtools - /usr/local/bin/samtools
[20:47:17] Found java - /usr/local/bin/java
[20:47:17] Found snpEff - /usr/local/bin/snpEff
[20:47:17] Found samclip - /usr/local/bin/samclip
[20:47:17] Found seqtk - /usr/local/bin/seqtk
[20:47:17] Found parallel - /usr/local/bin/parallel
[20:47:17] Found freebayes - /usr/local/bin/freebayes
[20:47:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:47:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:47:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:47:17] Found vcfuniq - /usr/local/bin/vcfuniq
[20:47:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:47:17] Found gzip - /bin/gzip
[20:47:17] Found vt - /usr/local/bin/vt
[20:47:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:47:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:47:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:47:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:47:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:47:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:47:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:47:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [16:12:47] This is snippy 4.6.0Show full stderr[16:12:47] This is snippy 4.6.0
[16:12:47] Written by Torsten Seemann
[16:12:47] Obtained from https://github.com/tseemann/snippy
[16:12:47] Detected operating system: linux
[16:12:47] Enabling bundled linux tools.
[16:12:47] Found bwa - /usr/local/bin/bwa
[16:12:47] Found bcftools - /usr/local/bin/bcftools
[16:12:47] Found samtools - /usr/local/bin/samtools
[16:12:47] Found java - /usr/local/bin/java
[16:12:47] Found snpEff - /usr/local/bin/snpEff
[16:12:47] Found samclip - /usr/local/bin/samclip
[16:12:47] Found seqtk - /usr/local/bin/seqtk
[16:12:47] Found parallel - /usr/local/bin/parallel
[16:12:47] Found freebayes - /usr/local/bin/freebayes
[16:12:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:12:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:12:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:12:47] Found vcfuniq - /usr/local/bin/vcfuniq
[16:12:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:12:47] Found gzip - /bin/gzip
[16:12:47] Found vt - /usr/local/bin/vt
[16:12:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:12:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:12:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:12:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:12:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:12:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:12:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:12:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [21:21:09] This is snippy 4.6.0Show full stderr[21:21:09] This is snippy 4.6.0
[21:21:09] Written by Torsten Seemann
[21:21:09] Obtained from https://github.com/tseemann/snippy
[21:21:09] Detected operating system: linux
[21:21:09] Enabling bundled linux tools.
[21:21:09] Found bwa - /usr/local/bin/bwa
[21:21:09] Found bcftools - /usr/local/bin/bcftools
[21:21:09] Found samtools - /usr/local/bin/samtools
[21:21:09] Found java - /usr/local/bin/java
[21:21:09] Found snpEff - /usr/local/bin/snpEff
[21:21:09] Found samclip - /usr/local/bin/samclip
[21:21:09] Found seqtk - /usr/local/bin/seqtk
[21:21:09] Found parallel - /usr/local/bin/parallel
[21:21:09] Found freebayes - /usr/local/bin/freebayes
[21:21:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:21:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:21:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:21:09] Found vcfuniq - /usr/local/bin/vcfuniq
[21:21:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:21:09] Found gzip - /bin/gzip
[21:21:09] Found vt - /usr/local/bin/vt
[21:21:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:21:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:21:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:21:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:21:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:21:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:21:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:21:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:43:50] This is snippy 4.6.0Show full stderr[00:43:50] This is snippy 4.6.0
[00:43:50] Written by Torsten Seemann
[00:43:50] Obtained from https://github.com/tseemann/snippy
[00:43:50] Detected operating system: linux
[00:43:50] Enabling bundled linux tools.
[00:43:50] Found bwa - /usr/local/bin/bwa
[00:43:50] Found bcftools - /usr/local/bin/bcftools
[00:43:50] Found samtools - /usr/local/bin/samtools
[00:43:50] Found java - /usr/local/bin/java
[00:43:50] Found snpEff - /usr/local/bin/snpEff
[00:43:50] Found samclip - /usr/local/bin/samclip
[00:43:50] Found seqtk - /usr/local/bin/seqtk
[00:43:50] Found parallel - /usr/local/bin/parallel
[00:43:50] Found freebayes - /usr/local/bin/freebayes
[00:43:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:43:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:43:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:43:50] Found vcfuniq - /usr/local/bin/vcfuniq
[00:43:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:43:50] Found gzip - /bin/gzip
[00:43:50] Found vt - /usr/local/bin/vt
[00:43:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:43:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:43:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:43:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:43:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:43:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:43:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:43:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:24:45] This is snippy 4.6.0Show full stderr[00:24:45] This is snippy 4.6.0
[00:24:45] Written by Torsten Seemann
[00:24:45] Obtained from https://github.com/tseemann/snippy
[00:24:45] Detected operating system: linux
[00:24:45] Enabling bundled linux tools.
[00:24:45] Found bwa - /usr/local/bin/bwa
[00:24:45] Found bcftools - /usr/local/bin/bcftools
[00:24:45] Found samtools - /usr/local/bin/samtools
[00:24:45] Found java - /usr/local/bin/java
[00:24:45] Found snpEff - /usr/local/bin/snpEff
[00:24:45] Found samclip - /usr/local/bin/samclip
[00:24:45] Found seqtk - /usr/local/bin/seqtk
[00:24:45] Found parallel - /usr/local/bin/parallel
[00:24:45] Found freebayes - /usr/local/bin/freebayes
[00:24:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:24:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:24:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:24:45] Found vcfuniq - /usr/local/bin/vcfuniq
[00:24:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:24:45] Found gzip - /bin/gzip
[00:24:45] Found vt - /usr/local/bin/vt
[00:24:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:24:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:24:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:24:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:24:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:24:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:24:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:24:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [09:34:49] This is snippy 4.6.0Show full stderr[09:34:49] This is snippy 4.6.0
[09:34:49] Written by Torsten Seemann
[09:34:49] Obtained from https://github.com/tseemann/snippy
[09:34:49] Detected operating system: linux
[09:34:49] Enabling bundled linux tools.
[09:34:49] Found bwa - /usr/local/bin/bwa
[09:34:49] Found bcftools - /usr/local/bin/bcftools
[09:34:49] Found samtools - /usr/local/bin/samtools
[09:34:49] Found java - /usr/local/bin/java
[09:34:49] Found snpEff - /usr/local/bin/snpEff
[09:34:49] Found samclip - /usr/local/bin/samclip
[09:34:49] Found seqtk - /usr/local/bin/seqtk
[09:34:49] Found parallel - /usr/local/bin/parallel
[09:34:49] Found freebayes - /usr/local/bin/freebayes
[09:34:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:34:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:34:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:34:49] Found vcfuniq - /usr/local/bin/vcfuniq
[09:34:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:34:49] Found gzip - /bin/gzip
[09:34:49] Found vt - /usr/local/bin/vt
[09:34:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:34:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:34:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:34:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:34:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:34:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:34:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:34:52] Using reference: /jetstream2/scratch/main/jobs/72478615/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat
[09:34:52] Treating reference as 'fasta' format.
[09:34:52] Will use 1 CPU cores.
[09:34:52] Using read file: /jetstream2/scratch/main/jobs/72478615/inputs/dataset_1dddc894-0e35-4e4b-b92d-42c90d918535.dat
[09:34:52] Using read file: /jetstream2/scratch/main/jobs/72478615/inputs/dataset_1dddc894-0e35-4e4b-b92d-42c90d918535.dat
[09:34:52] Creating folder: SCA4_21
[09:34:52] Changing working directory: SCA4_21
[09:34:52] Creating reference folder: reference
[09:34:52] Extracting FASTA and GFF from reference.
[09:34:53] Wrote 3 sequences to ref.fa
[09:34:53] Wrote 0 features to ref.gff
[09:34:53] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[09:34:53] Using BAM RG (Read Group) ID: SCA4_21
[09:34:53] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:34:53] Running: bwa index reference/ref.fa 2>> snps.log
[09:34:56] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:34:56] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:34:56] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:34:56] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:34:56] Running: bwa mem -Y -M -R '@RG\tID:SCA4_21\tSM:SCA4_21' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478615/inputs/dataset_1dddc894-0e35-4e4b-b92d-42c90d918535.dat /jetstream2/scratch/main/jobs/72478615/inputs/dataset_1dddc894-0e35-4e4b-b92d-42c90d918535.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478615/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478615/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478615/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: refere |
| 2 | [17:23:48] This is snippy 4.6.0Show full stderr[17:23:48] This is snippy 4.6.0
[17:23:48] Written by Torsten Seemann
[17:23:48] Obtained from https://github.com/tseemann/snippy
[17:23:48] Detected operating system: linux
[17:23:48] Enabling bundled linux tools.
[17:23:48] Found bwa - /usr/local/bin/bwa
[17:23:48] Found bcftools - /usr/local/bin/bcftools
[17:23:48] Found samtools - /usr/local/bin/samtools
[17:23:48] Found java - /usr/local/bin/java
[17:23:48] Found snpEff - /usr/local/bin/snpEff
[17:23:48] Found samclip - /usr/local/bin/samclip
[17:23:48] Found seqtk - /usr/local/bin/seqtk
[17:23:48] Found parallel - /usr/local/bin/parallel
[17:23:48] Found freebayes - /usr/local/bin/freebayes
[17:23:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:23:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:23:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:23:48] Found vcfuniq - /usr/local/bin/vcfuniq
[17:23:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:23:48] Found gzip - /bin/gzip
[17:23:48] Found vt - /usr/local/bin/vt
[17:23:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:23:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:23:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:23:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:23:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:23:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:23:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:23:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:24:27] This is snippy 4.6.0Show full stderr[17:24:27] This is snippy 4.6.0
[17:24:27] Written by Torsten Seemann
[17:24:27] Obtained from https://github.com/tseemann/snippy
[17:24:27] Detected operating system: linux
[17:24:27] Enabling bundled linux tools.
[17:24:27] Found bwa - /usr/local/bin/bwa
[17:24:27] Found bcftools - /usr/local/bin/bcftools
[17:24:27] Found samtools - /usr/local/bin/samtools
[17:24:27] Found java - /usr/local/bin/java
[17:24:27] Found snpEff - /usr/local/bin/snpEff
[17:24:27] Found samclip - /usr/local/bin/samclip
[17:24:27] Found seqtk - /usr/local/bin/seqtk
[17:24:27] Found parallel - /usr/local/bin/parallel
[17:24:27] Found freebayes - /usr/local/bin/freebayes
[17:24:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:27] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:27] Found gzip - /bin/gzip
[17:24:27] Found vt - /usr/local/bin/vt
[17:24:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:27:28] This is snippy 4.6.0Show full stderr[17:27:28] This is snippy 4.6.0
[17:27:28] Written by Torsten Seemann
[17:27:28] Obtained from https://github.com/tseemann/snippy
[17:27:28] Detected operating system: linux
[17:27:28] Enabling bundled linux tools.
[17:27:28] Found bwa - /usr/local/bin/bwa
[17:27:28] Found bcftools - /usr/local/bin/bcftools
[17:27:28] Found samtools - /usr/local/bin/samtools
[17:27:28] Found java - /usr/local/bin/java
[17:27:28] Found snpEff - /usr/local/bin/snpEff
[17:27:28] Found samclip - /usr/local/bin/samclip
[17:27:28] Found seqtk - /usr/local/bin/seqtk
[17:27:28] Found parallel - /usr/local/bin/parallel
[17:27:28] Found freebayes - /usr/local/bin/freebayes
[17:27:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:27:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:27:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:27:28] Found vcfuniq - /usr/local/bin/vcfuniq
[17:27:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:27:28] Found gzip - /bin/gzip
[17:27:28] Found vt - /usr/local/bin/vt
[17:27:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:27:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:27:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:27:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:27:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:27:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:27:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:27:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:49:04] This is snippy 4.6.0Show full stderr[17:49:04] This is snippy 4.6.0
[17:49:04] Written by Torsten Seemann
[17:49:04] Obtained from https://github.com/tseemann/snippy
[17:49:04] Detected operating system: linux
[17:49:04] Enabling bundled linux tools.
[17:49:04] Found bwa - /usr/local/bin/bwa
[17:49:04] Found bcftools - /usr/local/bin/bcftools
[17:49:04] Found samtools - /usr/local/bin/samtools
[17:49:04] Found java - /usr/local/bin/java
[17:49:04] Found snpEff - /usr/local/bin/snpEff
[17:49:04] Found samclip - /usr/local/bin/samclip
[17:49:04] Found seqtk - /usr/local/bin/seqtk
[17:49:04] Found parallel - /usr/local/bin/parallel
[17:49:04] Found freebayes - /usr/local/bin/freebayes
[17:49:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:49:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:49:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:49:04] Found vcfuniq - /usr/local/bin/vcfuniq
[17:49:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:49:04] Found gzip - /bin/gzip
[17:49:04] Found vt - /usr/local/bin/vt
[17:49:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:49:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:49:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:49:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:49:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:49:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:49:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:49:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:23:51] This is snippy 4.6.0Show full stderr[17:23:51] This is snippy 4.6.0
[17:23:51] Written by Torsten Seemann
[17:23:51] Obtained from https://github.com/tseemann/snippy
[17:23:51] Detected operating system: linux
[17:23:51] Enabling bundled linux tools.
[17:23:51] Found bwa - /usr/local/bin/bwa
[17:23:51] Found bcftools - /usr/local/bin/bcftools
[17:23:51] Found samtools - /usr/local/bin/samtools
[17:23:51] Found java - /usr/local/bin/java
[17:23:51] Found snpEff - /usr/local/bin/snpEff
[17:23:51] Found samclip - /usr/local/bin/samclip
[17:23:51] Found seqtk - /usr/local/bin/seqtk
[17:23:51] Found parallel - /usr/local/bin/parallel
[17:23:51] Found freebayes - /usr/local/bin/freebayes
[17:23:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:23:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:23:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:23:51] Found vcfuniq - /usr/local/bin/vcfuniq
[17:23:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:23:51] Found gzip - /bin/gzip
[17:23:51] Found vt - /usr/local/bin/vt
[17:23:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:23:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:23:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:23:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:23:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:23:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:23:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:23:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:23:59] This is snippy 4.6.0Show full stderr[17:23:59] This is snippy 4.6.0
[17:23:59] Written by Torsten Seemann
[17:23:59] Obtained from https://github.com/tseemann/snippy
[17:23:59] Detected operating system: linux
[17:23:59] Enabling bundled linux tools.
[17:23:59] Found bwa - /usr/local/bin/bwa
[17:23:59] Found bcftools - /usr/local/bin/bcftools
[17:23:59] Found samtools - /usr/local/bin/samtools
[17:23:59] Found java - /usr/local/bin/java
[17:23:59] Found snpEff - /usr/local/bin/snpEff
[17:23:59] Found samclip - /usr/local/bin/samclip
[17:23:59] Found seqtk - /usr/local/bin/seqtk
[17:23:59] Found parallel - /usr/local/bin/parallel
[17:23:59] Found freebayes - /usr/local/bin/freebayes
[17:23:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:23:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:23:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:23:59] Found vcfuniq - /usr/local/bin/vcfuniq
[17:23:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:23:59] Found gzip - /bin/gzip
[17:23:59] Found vt - /usr/local/bin/vt
[17:23:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:23:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:25:21] This is snippy 4.6.0Show full stderr[17:25:21] This is snippy 4.6.0
[17:25:21] Written by Torsten Seemann
[17:25:21] Obtained from https://github.com/tseemann/snippy
[17:25:21] Detected operating system: linux
[17:25:21] Enabling bundled linux tools.
[17:25:21] Found bwa - /usr/local/bin/bwa
[17:25:21] Found bcftools - /usr/local/bin/bcftools
[17:25:21] Found samtools - /usr/local/bin/samtools
[17:25:21] Found java - /usr/local/bin/java
[17:25:21] Found snpEff - /usr/local/bin/snpEff
[17:25:21] Found samclip - /usr/local/bin/samclip
[17:25:21] Found seqtk - /usr/local/bin/seqtk
[17:25:21] Found parallel - /usr/local/bin/parallel
[17:25:21] Found freebayes - /usr/local/bin/freebayes
[17:25:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:21] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:21] Found gzip - /bin/gzip
[17:25:21] Found vt - /usr/local/bin/vt
[17:25:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:29:17] This is snippy 4.6.0Show full stderr[17:29:17] This is snippy 4.6.0
[17:29:17] Written by Torsten Seemann
[17:29:17] Obtained from https://github.com/tseemann/snippy
[17:29:17] Detected operating system: linux
[17:29:17] Enabling bundled linux tools.
[17:29:17] Found bwa - /usr/local/bin/bwa
[17:29:17] Found bcftools - /usr/local/bin/bcftools
[17:29:17] Found samtools - /usr/local/bin/samtools
[17:29:17] Found java - /usr/local/bin/java
[17:29:17] Found snpEff - /usr/local/bin/snpEff
[17:29:17] Found samclip - /usr/local/bin/samclip
[17:29:17] Found seqtk - /usr/local/bin/seqtk
[17:29:17] Found parallel - /usr/local/bin/parallel
[17:29:17] Found freebayes - /usr/local/bin/freebayes
[17:29:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:29:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:29:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:29:17] Found vcfuniq - /usr/local/bin/vcfuniq
[17:29:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:29:17] Found gzip - /bin/gzip
[17:29:17] Found vt - /usr/local/bin/vt
[17:29:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:29:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:29:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:29:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:29:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:29:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:29:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:29:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:29:36] This is snippy 4.6.0Show full stderr[17:29:36] This is snippy 4.6.0
[17:29:36] Written by Torsten Seemann
[17:29:36] Obtained from https://github.com/tseemann/snippy
[17:29:36] Detected operating system: linux
[17:29:36] Enabling bundled linux tools.
[17:29:36] Found bwa - /usr/local/bin/bwa
[17:29:36] Found bcftools - /usr/local/bin/bcftools
[17:29:36] Found samtools - /usr/local/bin/samtools
[17:29:36] Found java - /usr/local/bin/java
[17:29:36] Found snpEff - /usr/local/bin/snpEff
[17:29:36] Found samclip - /usr/local/bin/samclip
[17:29:36] Found seqtk - /usr/local/bin/seqtk
[17:29:36] Found parallel - /usr/local/bin/parallel
[17:29:36] Found freebayes - /usr/local/bin/freebayes
[17:29:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:29:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:29:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:29:36] Found vcfuniq - /usr/local/bin/vcfuniq
[17:29:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:29:36] Found gzip - /bin/gzip
[17:29:36] Found vt - /usr/local/bin/vt
[17:29:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:29:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:29:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:29:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:29:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:29:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:29:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:29:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:30:23] This is snippy 4.6.0Show full stderr[17:30:23] This is snippy 4.6.0
[17:30:23] Written by Torsten Seemann
[17:30:23] Obtained from https://github.com/tseemann/snippy
[17:30:23] Detected operating system: linux
[17:30:23] Enabling bundled linux tools.
[17:30:23] Found bwa - /usr/local/bin/bwa
[17:30:23] Found bcftools - /usr/local/bin/bcftools
[17:30:23] Found samtools - /usr/local/bin/samtools
[17:30:23] Found java - /usr/local/bin/java
[17:30:23] Found snpEff - /usr/local/bin/snpEff
[17:30:23] Found samclip - /usr/local/bin/samclip
[17:30:23] Found seqtk - /usr/local/bin/seqtk
[17:30:23] Found parallel - /usr/local/bin/parallel
[17:30:23] Found freebayes - /usr/local/bin/freebayes
[17:30:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:30:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:30:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:30:23] Found vcfuniq - /usr/local/bin/vcfuniq
[17:30:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:30:23] Found gzip - /bin/gzip
[17:30:23] Found vt - /usr/local/bin/vt
[17:30:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:30:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:30:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:30:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:30:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:30:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:30:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:30:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:39:54] This is snippy 4.6.0Show full stderr[17:39:54] This is snippy 4.6.0
[17:39:54] Written by Torsten Seemann
[17:39:54] Obtained from https://github.com/tseemann/snippy
[17:39:54] Detected operating system: linux
[17:39:54] Enabling bundled linux tools.
[17:39:54] Found bwa - /usr/local/bin/bwa
[17:39:54] Found bcftools - /usr/local/bin/bcftools
[17:39:54] Found samtools - /usr/local/bin/samtools
[17:39:54] Found java - /usr/local/bin/java
[17:39:54] Found snpEff - /usr/local/bin/snpEff
[17:39:54] Found samclip - /usr/local/bin/samclip
[17:39:54] Found seqtk - /usr/local/bin/seqtk
[17:39:54] Found parallel - /usr/local/bin/parallel
[17:39:54] Found freebayes - /usr/local/bin/freebayes
[17:39:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:39:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:39:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:39:54] Found vcfuniq - /usr/local/bin/vcfuniq
[17:39:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:39:54] Found gzip - /bin/gzip
[17:39:54] Found vt - /usr/local/bin/vt
[17:39:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:39:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:39:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:39:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:39:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:39:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:39:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:39:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:41:06] This is snippy 4.6.0Show full stderr[17:41:06] This is snippy 4.6.0
[17:41:06] Written by Torsten Seemann
[17:41:06] Obtained from https://github.com/tseemann/snippy
[17:41:06] Detected operating system: linux
[17:41:06] Enabling bundled linux tools.
[17:41:06] Found bwa - /usr/local/bin/bwa
[17:41:06] Found bcftools - /usr/local/bin/bcftools
[17:41:06] Found samtools - /usr/local/bin/samtools
[17:41:06] Found java - /usr/local/bin/java
[17:41:06] Found snpEff - /usr/local/bin/snpEff
[17:41:06] Found samclip - /usr/local/bin/samclip
[17:41:06] Found seqtk - /usr/local/bin/seqtk
[17:41:07] Found parallel - /usr/local/bin/parallel
[17:41:07] Found freebayes - /usr/local/bin/freebayes
[17:41:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:41:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:41:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:41:07] Found vcfuniq - /usr/local/bin/vcfuniq
[17:41:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:41:07] Found gzip - /bin/gzip
[17:41:07] Found vt - /usr/local/bin/vt
[17:41:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:41:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:41:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:41:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:41:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:41:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:41:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:41:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:41:34] This is snippy 4.6.0Show full stderr[17:41:34] This is snippy 4.6.0
[17:41:34] Written by Torsten Seemann
[17:41:34] Obtained from https://github.com/tseemann/snippy
[17:41:34] Detected operating system: linux
[17:41:34] Enabling bundled linux tools.
[17:41:34] Found bwa - /usr/local/bin/bwa
[17:41:34] Found bcftools - /usr/local/bin/bcftools
[17:41:34] Found samtools - /usr/local/bin/samtools
[17:41:34] Found java - /usr/local/bin/java
[17:41:34] Found snpEff - /usr/local/bin/snpEff
[17:41:34] Found samclip - /usr/local/bin/samclip
[17:41:34] Found seqtk - /usr/local/bin/seqtk
[17:41:34] Found parallel - /usr/local/bin/parallel
[17:41:34] Found freebayes - /usr/local/bin/freebayes
[17:41:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:41:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:41:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:41:34] Found vcfuniq - /usr/local/bin/vcfuniq
[17:41:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:41:34] Found gzip - /bin/gzip
[17:41:34] Found vt - /usr/local/bin/vt
[17:41:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:41:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:41:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:41:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:41:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:41:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:41:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:41:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:38:54] This is snippy 4.6.0Show full stderr[17:38:54] This is snippy 4.6.0
[17:38:54] Written by Torsten Seemann
[17:38:54] Obtained from https://github.com/tseemann/snippy
[17:38:54] Detected operating system: linux
[17:38:54] Enabling bundled linux tools.
[17:38:54] Found bwa - /usr/local/bin/bwa
[17:38:54] Found bcftools - /usr/local/bin/bcftools
[17:38:54] Found samtools - /usr/local/bin/samtools
[17:38:54] Found java - /usr/local/bin/java
[17:38:54] Found snpEff - /usr/local/bin/snpEff
[17:38:54] Found samclip - /usr/local/bin/samclip
[17:38:55] Found seqtk - /usr/local/bin/seqtk
[17:38:55] Found parallel - /usr/local/bin/parallel
[17:38:55] Found freebayes - /usr/local/bin/freebayes
[17:38:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:38:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:38:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:38:55] Found vcfuniq - /usr/local/bin/vcfuniq
[17:38:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:38:55] Found gzip - /bin/gzip
[17:38:55] Found vt - /usr/local/bin/vt
[17:38:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:38:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:38:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:38:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:38:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:38:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:38:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:38:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:41:21] This is snippy 4.6.0Show full stderr[17:41:21] This is snippy 4.6.0
[17:41:21] Written by Torsten Seemann
[17:41:21] Obtained from https://github.com/tseemann/snippy
[17:41:21] Detected operating system: linux
[17:41:21] Enabling bundled linux tools.
[17:41:21] Found bwa - /usr/local/bin/bwa
[17:41:21] Found bcftools - /usr/local/bin/bcftools
[17:41:21] Found samtools - /usr/local/bin/samtools
[17:41:21] Found java - /usr/local/bin/java
[17:41:21] Found snpEff - /usr/local/bin/snpEff
[17:41:22] Found samclip - /usr/local/bin/samclip
[17:41:22] Found seqtk - /usr/local/bin/seqtk
[17:41:22] Found parallel - /usr/local/bin/parallel
[17:41:22] Found freebayes - /usr/local/bin/freebayes
[17:41:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:41:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:41:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:41:22] Found vcfuniq - /usr/local/bin/vcfuniq
[17:41:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:41:22] Found gzip - /bin/gzip
[17:41:22] Found vt - /usr/local/bin/vt
[17:41:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:41:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:41:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:41:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:41:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:41:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:41:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:41:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:42:45] This is snippy 4.6.0Show full stderr[17:42:45] This is snippy 4.6.0
[17:42:45] Written by Torsten Seemann
[17:42:45] Obtained from https://github.com/tseemann/snippy
[17:42:45] Detected operating system: linux
[17:42:45] Enabling bundled linux tools.
[17:42:45] Found bwa - /usr/local/bin/bwa
[17:42:45] Found bcftools - /usr/local/bin/bcftools
[17:42:45] Found samtools - /usr/local/bin/samtools
[17:42:45] Found java - /usr/local/bin/java
[17:42:45] Found snpEff - /usr/local/bin/snpEff
[17:42:45] Found samclip - /usr/local/bin/samclip
[17:42:45] Found seqtk - /usr/local/bin/seqtk
[17:42:45] Found parallel - /usr/local/bin/parallel
[17:42:45] Found freebayes - /usr/local/bin/freebayes
[17:42:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:42:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:42:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:42:45] Found vcfuniq - /usr/local/bin/vcfuniq
[17:42:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:42:45] Found gzip - /bin/gzip
[17:42:45] Found vt - /usr/local/bin/vt
[17:42:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:42:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:42:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:42:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:42:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:42:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:42:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:42:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:44:58] This is snippy 4.6.0Show full stderr[17:44:58] This is snippy 4.6.0
[17:44:58] Written by Torsten Seemann
[17:44:58] Obtained from https://github.com/tseemann/snippy
[17:44:58] Detected operating system: linux
[17:44:58] Enabling bundled linux tools.
[17:44:58] Found bwa - /usr/local/bin/bwa
[17:44:58] Found bcftools - /usr/local/bin/bcftools
[17:44:58] Found samtools - /usr/local/bin/samtools
[17:44:58] Found java - /usr/local/bin/java
[17:44:58] Found snpEff - /usr/local/bin/snpEff
[17:44:58] Found samclip - /usr/local/bin/samclip
[17:44:58] Found seqtk - /usr/local/bin/seqtk
[17:44:58] Found parallel - /usr/local/bin/parallel
[17:44:59] Found freebayes - /usr/local/bin/freebayes
[17:44:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:44:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:44:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:44:59] Found vcfuniq - /usr/local/bin/vcfuniq
[17:44:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:44:59] Found gzip - /bin/gzip
[17:44:59] Found vt - /usr/local/bin/vt
[17:44:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:44:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:44:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:44:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:44:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:40:45] This is snippy 4.6.0Show full stderr[17:40:45] This is snippy 4.6.0
[17:40:45] Written by Torsten Seemann
[17:40:45] Obtained from https://github.com/tseemann/snippy
[17:40:45] Detected operating system: linux
[17:40:45] Enabling bundled linux tools.
[17:40:45] Found bwa - /usr/local/bin/bwa
[17:40:45] Found bcftools - /usr/local/bin/bcftools
[17:40:45] Found samtools - /usr/local/bin/samtools
[17:40:45] Found java - /usr/local/bin/java
[17:40:45] Found snpEff - /usr/local/bin/snpEff
[17:40:45] Found samclip - /usr/local/bin/samclip
[17:40:45] Found seqtk - /usr/local/bin/seqtk
[17:40:45] Found parallel - /usr/local/bin/parallel
[17:40:45] Found freebayes - /usr/local/bin/freebayes
[17:40:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:40:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:40:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:40:45] Found vcfuniq - /usr/local/bin/vcfuniq
[17:40:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:40:45] Found gzip - /bin/gzip
[17:40:45] Found vt - /usr/local/bin/vt
[17:40:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:40:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:40:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:40:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:40:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:40:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:40:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:40:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:37:54] This is snippy 4.6.0Show full stderr[17:37:54] This is snippy 4.6.0
[17:37:54] Written by Torsten Seemann
[17:37:54] Obtained from https://github.com/tseemann/snippy
[17:37:54] Detected operating system: linux
[17:37:54] Enabling bundled linux tools.
[17:37:54] Found bwa - /usr/local/bin/bwa
[17:37:54] Found bcftools - /usr/local/bin/bcftools
[17:37:54] Found samtools - /usr/local/bin/samtools
[17:37:54] Found java - /usr/local/bin/java
[17:37:54] Found snpEff - /usr/local/bin/snpEff
[17:37:54] Found samclip - /usr/local/bin/samclip
[17:37:54] Found seqtk - /usr/local/bin/seqtk
[17:37:54] Found parallel - /usr/local/bin/parallel
[17:37:54] Found freebayes - /usr/local/bin/freebayes
[17:37:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:37:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:37:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:37:54] Found vcfuniq - /usr/local/bin/vcfuniq
[17:37:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:37:54] Found gzip - /bin/gzip
[17:37:54] Found vt - /usr/local/bin/vt
[17:37:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:37:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:37:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:37:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:37:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:37:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:37:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:37:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:43:38] This is snippy 4.6.0Show full stderr[17:43:38] This is snippy 4.6.0
[17:43:38] Written by Torsten Seemann
[17:43:38] Obtained from https://github.com/tseemann/snippy
[17:43:38] Detected operating system: linux
[17:43:38] Enabling bundled linux tools.
[17:43:38] Found bwa - /usr/local/bin/bwa
[17:43:38] Found bcftools - /usr/local/bin/bcftools
[17:43:38] Found samtools - /usr/local/bin/samtools
[17:43:38] Found java - /usr/local/bin/java
[17:43:38] Found snpEff - /usr/local/bin/snpEff
[17:43:38] Found samclip - /usr/local/bin/samclip
[17:43:38] Found seqtk - /usr/local/bin/seqtk
[17:43:38] Found parallel - /usr/local/bin/parallel
[17:43:38] Found freebayes - /usr/local/bin/freebayes
[17:43:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:43:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:43:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:43:39] Found vcfuniq - /usr/local/bin/vcfuniq
[17:43:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:43:39] Found gzip - /bin/gzip
[17:43:39] Found vt - /usr/local/bin/vt
[17:43:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:43:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:43:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:43:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:43:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:43:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:43:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:43:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [17:48:46] This is snippy 4.6.0Show full stderr[17:48:46] This is snippy 4.6.0
[17:48:46] Written by Torsten Seemann
[17:48:46] Obtained from https://github.com/tseemann/snippy
[17:48:46] Detected operating system: linux
[17:48:46] Enabling bundled linux tools.
[17:48:46] Found bwa - /usr/local/bin/bwa
[17:48:46] Found bcftools - /usr/local/bin/bcftools
[17:48:46] Found samtools - /usr/local/bin/samtools
[17:48:46] Found java - /usr/local/bin/java
[17:48:46] Found snpEff - /usr/local/bin/snpEff
[17:48:46] Found samclip - /usr/local/bin/samclip
[17:48:46] Found seqtk - /usr/local/bin/seqtk
[17:48:46] Found parallel - /usr/local/bin/parallel
[17:48:46] Found freebayes - /usr/local/bin/freebayes
[17:48:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:48:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:48:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:48:46] Found vcfuniq - /usr/local/bin/vcfuniq
[17:48:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:48:46] Found gzip - /bin/gzip
[17:48:46] Found vt - /usr/local/bin/vt
[17:48:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:48:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:48:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:48:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:48:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:48:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:48:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:48:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:23:35] This is snippy 4.6.0Show full stderr[00:23:35] This is snippy 4.6.0
[00:23:35] Written by Torsten Seemann
[00:23:35] Obtained from https://github.com/tseemann/snippy
[00:23:35] Detected operating system: linux
[00:23:35] Enabling bundled linux tools.
[00:23:35] Found bwa - /usr/local/bin/bwa
[00:23:35] Found bcftools - /usr/local/bin/bcftools
[00:23:35] Found samtools - /usr/local/bin/samtools
[00:23:35] Found java - /usr/local/bin/java
[00:23:35] Found snpEff - /usr/local/bin/snpEff
[00:23:35] Found samclip - /usr/local/bin/samclip
[00:23:35] Found seqtk - /usr/local/bin/seqtk
[00:23:35] Found parallel - /usr/local/bin/parallel
[00:23:35] Found freebayes - /usr/local/bin/freebayes
[00:23:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:35] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:35] Found gzip - /bin/gzip
[00:23:35] Found vt - /usr/local/bin/vt
[00:23:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:23:45] This is snippy 4.6.0Show full stderr[00:23:45] This is snippy 4.6.0
[00:23:45] Written by Torsten Seemann
[00:23:45] Obtained from https://github.com/tseemann/snippy
[00:23:45] Detected operating system: linux
[00:23:45] Enabling bundled linux tools.
[00:23:45] Found bwa - /usr/local/bin/bwa
[00:23:45] Found bcftools - /usr/local/bin/bcftools
[00:23:45] Found samtools - /usr/local/bin/samtools
[00:23:45] Found java - /usr/local/bin/java
[00:23:45] Found snpEff - /usr/local/bin/snpEff
[00:23:45] Found samclip - /usr/local/bin/samclip
[00:23:45] Found seqtk - /usr/local/bin/seqtk
[00:23:45] Found parallel - /usr/local/bin/parallel
[00:23:45] Found freebayes - /usr/local/bin/freebayes
[00:23:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:45] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:45] Found gzip - /bin/gzip
[00:23:45] Found vt - /usr/local/bin/vt
[00:23:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:23:57] This is snippy 4.6.0Show full stderr[00:23:57] This is snippy 4.6.0
[00:23:57] Written by Torsten Seemann
[00:23:57] Obtained from https://github.com/tseemann/snippy
[00:23:57] Detected operating system: linux
[00:23:57] Enabling bundled linux tools.
[00:23:57] Found bwa - /usr/local/bin/bwa
[00:23:57] Found bcftools - /usr/local/bin/bcftools
[00:23:57] Found samtools - /usr/local/bin/samtools
[00:23:57] Found java - /usr/local/bin/java
[00:23:57] Found snpEff - /usr/local/bin/snpEff
[00:23:57] Found samclip - /usr/local/bin/samclip
[00:23:57] Found seqtk - /usr/local/bin/seqtk
[00:23:57] Found parallel - /usr/local/bin/parallel
[00:23:57] Found freebayes - /usr/local/bin/freebayes
[00:23:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:57] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:57] Found gzip - /bin/gzip
[00:23:57] Found vt - /usr/local/bin/vt
[00:23:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:24:00] This is snippy 4.6.0Show full stderr[00:24:00] This is snippy 4.6.0
[00:24:00] Written by Torsten Seemann
[00:24:00] Obtained from https://github.com/tseemann/snippy
[00:24:00] Detected operating system: linux
[00:24:00] Enabling bundled linux tools.
[00:24:00] Found bwa - /usr/local/bin/bwa
[00:24:00] Found bcftools - /usr/local/bin/bcftools
[00:24:00] Found samtools - /usr/local/bin/samtools
[00:24:00] Found java - /usr/local/bin/java
[00:24:00] Found snpEff - /usr/local/bin/snpEff
[00:24:00] Found samclip - /usr/local/bin/samclip
[00:24:00] Found seqtk - /usr/local/bin/seqtk
[00:24:00] Found parallel - /usr/local/bin/parallel
[00:24:00] Found freebayes - /usr/local/bin/freebayes
[00:24:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:24:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:24:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:24:00] Found vcfuniq - /usr/local/bin/vcfuniq
[00:24:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:24:00] Found gzip - /bin/gzip
[00:24:00] Found vt - /usr/local/bin/vt
[00:24:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:24:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:24:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:24:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:24:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:24:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:24:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:24:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:24:12] This is snippy 4.6.0Show full stderr[00:24:12] This is snippy 4.6.0
[00:24:12] Written by Torsten Seemann
[00:24:12] Obtained from https://github.com/tseemann/snippy
[00:24:12] Detected operating system: linux
[00:24:12] Enabling bundled linux tools.
[00:24:12] Found bwa - /usr/local/bin/bwa
[00:24:12] Found bcftools - /usr/local/bin/bcftools
[00:24:12] Found samtools - /usr/local/bin/samtools
[00:24:12] Found java - /usr/local/bin/java
[00:24:12] Found snpEff - /usr/local/bin/snpEff
[00:24:12] Found samclip - /usr/local/bin/samclip
[00:24:12] Found seqtk - /usr/local/bin/seqtk
[00:24:12] Found parallel - /usr/local/bin/parallel
[00:24:12] Found freebayes - /usr/local/bin/freebayes
[00:24:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:24:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:24:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:24:12] Found vcfuniq - /usr/local/bin/vcfuniq
[00:24:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:24:12] Found gzip - /bin/gzip
[00:24:12] Found vt - /usr/local/bin/vt
[00:24:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:24:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:24:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:24:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:24:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:24:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:24:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:24:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:24:15] This is snippy 4.6.0Show full stderr[00:24:15] This is snippy 4.6.0
[00:24:15] Written by Torsten Seemann
[00:24:15] Obtained from https://github.com/tseemann/snippy
[00:24:15] Detected operating system: linux
[00:24:15] Enabling bundled linux tools.
[00:24:15] Found bwa - /usr/local/bin/bwa
[00:24:15] Found bcftools - /usr/local/bin/bcftools
[00:24:15] Found samtools - /usr/local/bin/samtools
[00:24:15] Found java - /usr/local/bin/java
[00:24:15] Found snpEff - /usr/local/bin/snpEff
[00:24:15] Found samclip - /usr/local/bin/samclip
[00:24:15] Found seqtk - /usr/local/bin/seqtk
[00:24:15] Found parallel - /usr/local/bin/parallel
[00:24:15] Found freebayes - /usr/local/bin/freebayes
[00:24:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:24:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:24:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:24:15] Found vcfuniq - /usr/local/bin/vcfuniq
[00:24:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:24:15] Found gzip - /bin/gzip
[00:24:15] Found vt - /usr/local/bin/vt
[00:24:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:24:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:24:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:24:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:24:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:24:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:24:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:24:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:24:43] This is snippy 4.6.0Show full stderr[00:24:43] This is snippy 4.6.0
[00:24:43] Written by Torsten Seemann
[00:24:43] Obtained from https://github.com/tseemann/snippy
[00:24:43] Detected operating system: linux
[00:24:43] Enabling bundled linux tools.
[00:24:43] Found bwa - /usr/local/bin/bwa
[00:24:43] Found bcftools - /usr/local/bin/bcftools
[00:24:43] Found samtools - /usr/local/bin/samtools
[00:24:43] Found java - /usr/local/bin/java
[00:24:43] Found snpEff - /usr/local/bin/snpEff
[00:24:43] Found samclip - /usr/local/bin/samclip
[00:24:43] Found seqtk - /usr/local/bin/seqtk
[00:24:43] Found parallel - /usr/local/bin/parallel
[00:24:43] Found freebayes - /usr/local/bin/freebayes
[00:24:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:24:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:24:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:24:43] Found vcfuniq - /usr/local/bin/vcfuniq
[00:24:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:24:43] Found gzip - /bin/gzip
[00:24:43] Found vt - /usr/local/bin/vt
[00:24:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:24:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:24:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:24:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:24:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:24:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:24:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:24:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:25:33] This is snippy 4.6.0Show full stderr[00:25:33] This is snippy 4.6.0
[00:25:33] Written by Torsten Seemann
[00:25:33] Obtained from https://github.com/tseemann/snippy
[00:25:33] Detected operating system: linux
[00:25:33] Enabling bundled linux tools.
[00:25:33] Found bwa - /usr/local/bin/bwa
[00:25:33] Found bcftools - /usr/local/bin/bcftools
[00:25:33] Found samtools - /usr/local/bin/samtools
[00:25:33] Found java - /usr/local/bin/java
[00:25:33] Found snpEff - /usr/local/bin/snpEff
[00:25:33] Found samclip - /usr/local/bin/samclip
[00:25:33] Found seqtk - /usr/local/bin/seqtk
[00:25:33] Found parallel - /usr/local/bin/parallel
[00:25:33] Found freebayes - /usr/local/bin/freebayes
[00:25:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:25:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:25:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:25:33] Found vcfuniq - /usr/local/bin/vcfuniq
[00:25:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:25:33] Found gzip - /bin/gzip
[00:25:33] Found vt - /usr/local/bin/vt
[00:25:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:25:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:25:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:25:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:25:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:25:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:25:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:25:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:26:21] This is snippy 4.6.0Show full stderr[00:26:21] This is snippy 4.6.0
[00:26:21] Written by Torsten Seemann
[00:26:21] Obtained from https://github.com/tseemann/snippy
[00:26:21] Detected operating system: linux
[00:26:21] Enabling bundled linux tools.
[00:26:21] Found bwa - /usr/local/bin/bwa
[00:26:21] Found bcftools - /usr/local/bin/bcftools
[00:26:21] Found samtools - /usr/local/bin/samtools
[00:26:21] Found java - /usr/local/bin/java
[00:26:21] Found snpEff - /usr/local/bin/snpEff
[00:26:21] Found samclip - /usr/local/bin/samclip
[00:26:21] Found seqtk - /usr/local/bin/seqtk
[00:26:21] Found parallel - /usr/local/bin/parallel
[00:26:21] Found freebayes - /usr/local/bin/freebayes
[00:26:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:21] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:21] Found gzip - /bin/gzip
[00:26:21] Found vt - /usr/local/bin/vt
[00:26:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:26:48] This is snippy 4.6.0Show full stderr[00:26:48] This is snippy 4.6.0
[00:26:48] Written by Torsten Seemann
[00:26:48] Obtained from https://github.com/tseemann/snippy
[00:26:48] Detected operating system: linux
[00:26:48] Enabling bundled linux tools.
[00:26:48] Found bwa - /usr/local/bin/bwa
[00:26:48] Found bcftools - /usr/local/bin/bcftools
[00:26:48] Found samtools - /usr/local/bin/samtools
[00:26:48] Found java - /usr/local/bin/java
[00:26:48] Found snpEff - /usr/local/bin/snpEff
[00:26:48] Found samclip - /usr/local/bin/samclip
[00:26:48] Found seqtk - /usr/local/bin/seqtk
[00:26:48] Found parallel - /usr/local/bin/parallel
[00:26:48] Found freebayes - /usr/local/bin/freebayes
[00:26:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:48] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:48] Found gzip - /bin/gzip
[00:26:48] Found vt - /usr/local/bin/vt
[00:26:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:27:27] This is snippy 4.6.0Show full stderr[00:27:27] This is snippy 4.6.0
[00:27:27] Written by Torsten Seemann
[00:27:27] Obtained from https://github.com/tseemann/snippy
[00:27:27] Detected operating system: linux
[00:27:27] Enabling bundled linux tools.
[00:27:27] Found bwa - /usr/local/bin/bwa
[00:27:27] Found bcftools - /usr/local/bin/bcftools
[00:27:27] Found samtools - /usr/local/bin/samtools
[00:27:27] Found java - /usr/local/bin/java
[00:27:27] Found snpEff - /usr/local/bin/snpEff
[00:27:27] Found samclip - /usr/local/bin/samclip
[00:27:27] Found seqtk - /usr/local/bin/seqtk
[00:27:27] Found parallel - /usr/local/bin/parallel
[00:27:27] Found freebayes - /usr/local/bin/freebayes
[00:27:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:27:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:27:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:27:27] Found vcfuniq - /usr/local/bin/vcfuniq
[00:27:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:27:27] Found gzip - /bin/gzip
[00:27:27] Found vt - /usr/local/bin/vt
[00:27:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:27:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:27:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:27:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:27:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:27:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:27:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:27:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:27:21] This is snippy 4.6.0Show full stderr[00:27:21] This is snippy 4.6.0
[00:27:21] Written by Torsten Seemann
[00:27:21] Obtained from https://github.com/tseemann/snippy
[00:27:21] Detected operating system: linux
[00:27:21] Enabling bundled linux tools.
[00:27:21] Found bwa - /usr/local/bin/bwa
[00:27:21] Found bcftools - /usr/local/bin/bcftools
[00:27:21] Found samtools - /usr/local/bin/samtools
[00:27:21] Found java - /usr/local/bin/java
[00:27:21] Found snpEff - /usr/local/bin/snpEff
[00:27:21] Found samclip - /usr/local/bin/samclip
[00:27:21] Found seqtk - /usr/local/bin/seqtk
[00:27:21] Found parallel - /usr/local/bin/parallel
[00:27:21] Found freebayes - /usr/local/bin/freebayes
[00:27:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:27:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:27:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:27:21] Found vcfuniq - /usr/local/bin/vcfuniq
[00:27:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:27:21] Found gzip - /bin/gzip
[00:27:21] Found vt - /usr/local/bin/vt
[00:27:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:27:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:27:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:27:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:27:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:27:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:27:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:27:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:29:57] This is snippy 4.6.0Show full stderr[00:29:57] This is snippy 4.6.0
[00:29:57] Written by Torsten Seemann
[00:29:57] Obtained from https://github.com/tseemann/snippy
[00:29:57] Detected operating system: linux
[00:29:57] Enabling bundled linux tools.
[00:29:57] Found bwa - /usr/local/bin/bwa
[00:29:57] Found bcftools - /usr/local/bin/bcftools
[00:29:57] Found samtools - /usr/local/bin/samtools
[00:29:57] Found java - /usr/local/bin/java
[00:29:57] Found snpEff - /usr/local/bin/snpEff
[00:29:57] Found samclip - /usr/local/bin/samclip
[00:29:57] Found seqtk - /usr/local/bin/seqtk
[00:29:57] Found parallel - /usr/local/bin/parallel
[00:29:57] Found freebayes - /usr/local/bin/freebayes
[00:29:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:57] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:57] Found gzip - /bin/gzip
[00:29:57] Found vt - /usr/local/bin/vt
[00:29:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:42:17] This is snippy 4.6.0Show full stderr[00:42:17] This is snippy 4.6.0
[00:42:17] Written by Torsten Seemann
[00:42:17] Obtained from https://github.com/tseemann/snippy
[00:42:17] Detected operating system: linux
[00:42:17] Enabling bundled linux tools.
[00:42:17] Found bwa - /usr/local/bin/bwa
[00:42:17] Found bcftools - /usr/local/bin/bcftools
[00:42:17] Found samtools - /usr/local/bin/samtools
[00:42:17] Found java - /usr/local/bin/java
[00:42:17] Found snpEff - /usr/local/bin/snpEff
[00:42:17] Found samclip - /usr/local/bin/samclip
[00:42:17] Found seqtk - /usr/local/bin/seqtk
[00:42:17] Found parallel - /usr/local/bin/parallel
[00:42:17] Found freebayes - /usr/local/bin/freebayes
[00:42:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:42:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:42:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:42:18] Found vcfuniq - /usr/local/bin/vcfuniq
[00:42:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:42:18] Found gzip - /bin/gzip
[00:42:18] Found vt - /usr/local/bin/vt
[00:42:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:42:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:42:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:42:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:42:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:42:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:42:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:42:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:32:51] This is snippy 4.6.0Show full stderr[00:32:51] This is snippy 4.6.0
[00:32:51] Written by Torsten Seemann
[00:32:51] Obtained from https://github.com/tseemann/snippy
[00:32:51] Detected operating system: linux
[00:32:51] Enabling bundled linux tools.
[00:32:51] Found bwa - /usr/local/bin/bwa
[00:32:51] Found bcftools - /usr/local/bin/bcftools
[00:32:51] Found samtools - /usr/local/bin/samtools
[00:32:51] Found java - /usr/local/bin/java
[00:32:51] Found snpEff - /usr/local/bin/snpEff
[00:32:51] Found samclip - /usr/local/bin/samclip
[00:32:51] Found seqtk - /usr/local/bin/seqtk
[00:32:51] Found parallel - /usr/local/bin/parallel
[00:32:51] Found freebayes - /usr/local/bin/freebayes
[00:32:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:32:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:32:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:32:51] Found vcfuniq - /usr/local/bin/vcfuniq
[00:32:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:32:51] Found gzip - /bin/gzip
[00:32:51] Found vt - /usr/local/bin/vt
[00:32:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:32:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:32:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:32:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:32:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:32:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:32:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:32:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:29:54] This is snippy 4.6.0Show full stderr[00:29:54] This is snippy 4.6.0
[00:29:54] Written by Torsten Seemann
[00:29:54] Obtained from https://github.com/tseemann/snippy
[00:29:54] Detected operating system: linux
[00:29:54] Enabling bundled linux tools.
[00:29:54] Found bwa - /usr/local/bin/bwa
[00:29:54] Found bcftools - /usr/local/bin/bcftools
[00:29:54] Found samtools - /usr/local/bin/samtools
[00:29:54] Found java - /usr/local/bin/java
[00:29:54] Found snpEff - /usr/local/bin/snpEff
[00:29:54] Found samclip - /usr/local/bin/samclip
[00:29:54] Found seqtk - /usr/local/bin/seqtk
[00:29:54] Found parallel - /usr/local/bin/parallel
[00:29:54] Found freebayes - /usr/local/bin/freebayes
[00:29:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:54] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:54] Found gzip - /bin/gzip
[00:29:54] Found vt - /usr/local/bin/vt
[00:29:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:30:09] This is snippy 4.6.0Show full stderr[00:30:09] This is snippy 4.6.0
[00:30:09] Written by Torsten Seemann
[00:30:09] Obtained from https://github.com/tseemann/snippy
[00:30:09] Detected operating system: linux
[00:30:09] Enabling bundled linux tools.
[00:30:09] Found bwa - /usr/local/bin/bwa
[00:30:09] Found bcftools - /usr/local/bin/bcftools
[00:30:09] Found samtools - /usr/local/bin/samtools
[00:30:09] Found java - /usr/local/bin/java
[00:30:09] Found snpEff - /usr/local/bin/snpEff
[00:30:09] Found samclip - /usr/local/bin/samclip
[00:30:09] Found seqtk - /usr/local/bin/seqtk
[00:30:09] Found parallel - /usr/local/bin/parallel
[00:30:09] Found freebayes - /usr/local/bin/freebayes
[00:30:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:30:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:30:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:30:09] Found vcfuniq - /usr/local/bin/vcfuniq
[00:30:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:30:09] Found gzip - /bin/gzip
[00:30:09] Found vt - /usr/local/bin/vt
[00:30:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:30:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:30:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:30:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:30:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:30:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:30:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:30:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:31:33] This is snippy 4.6.0Show full stderr[00:31:33] This is snippy 4.6.0
[00:31:33] Written by Torsten Seemann
[00:31:33] Obtained from https://github.com/tseemann/snippy
[00:31:33] Detected operating system: linux
[00:31:33] Enabling bundled linux tools.
[00:31:33] Found bwa - /usr/local/bin/bwa
[00:31:33] Found bcftools - /usr/local/bin/bcftools
[00:31:33] Found samtools - /usr/local/bin/samtools
[00:31:33] Found java - /usr/local/bin/java
[00:31:33] Found snpEff - /usr/local/bin/snpEff
[00:31:33] Found samclip - /usr/local/bin/samclip
[00:31:33] Found seqtk - /usr/local/bin/seqtk
[00:31:33] Found parallel - /usr/local/bin/parallel
[00:31:33] Found freebayes - /usr/local/bin/freebayes
[00:31:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:33] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:33] Found gzip - /bin/gzip
[00:31:33] Found vt - /usr/local/bin/vt
[00:31:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:28:31] This is snippy 4.6.0Show full stderr[00:28:31] This is snippy 4.6.0
[00:28:31] Written by Torsten Seemann
[00:28:31] Obtained from https://github.com/tseemann/snippy
[00:28:31] Detected operating system: linux
[00:28:31] Enabling bundled linux tools.
[00:28:31] Found bwa - /usr/local/bin/bwa
[00:28:31] Found bcftools - /usr/local/bin/bcftools
[00:28:31] Found samtools - /usr/local/bin/samtools
[00:28:31] Found java - /usr/local/bin/java
[00:28:31] Found snpEff - /usr/local/bin/snpEff
[00:28:31] Found samclip - /usr/local/bin/samclip
[00:28:31] Found seqtk - /usr/local/bin/seqtk
[00:28:31] Found parallel - /usr/local/bin/parallel
[00:28:31] Found freebayes - /usr/local/bin/freebayes
[00:28:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:28:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:28:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:28:31] Found vcfuniq - /usr/local/bin/vcfuniq
[00:28:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:28:31] Found gzip - /bin/gzip
[00:28:31] Found vt - /usr/local/bin/vt
[00:28:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:28:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:28:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:28:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:28:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:28:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:28:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:28:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:29:20] This is snippy 4.6.0Show full stderr[00:29:20] This is snippy 4.6.0
[00:29:20] Written by Torsten Seemann
[00:29:20] Obtained from https://github.com/tseemann/snippy
[00:29:20] Detected operating system: linux
[00:29:20] Enabling bundled linux tools.
[00:29:20] Found bwa - /usr/local/bin/bwa
[00:29:21] Found bcftools - /usr/local/bin/bcftools
[00:29:21] Found samtools - /usr/local/bin/samtools
[00:29:21] Found java - /usr/local/bin/java
[00:29:21] Found snpEff - /usr/local/bin/snpEff
[00:29:21] Found samclip - /usr/local/bin/samclip
[00:29:21] Found seqtk - /usr/local/bin/seqtk
[00:29:21] Found parallel - /usr/local/bin/parallel
[00:29:21] Found freebayes - /usr/local/bin/freebayes
[00:29:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:21] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:21] Found gzip - /bin/gzip
[00:29:21] Found vt - /usr/local/bin/vt
[00:29:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:32:04] This is snippy 4.6.0Show full stderr[00:32:04] This is snippy 4.6.0
[00:32:04] Written by Torsten Seemann
[00:32:04] Obtained from https://github.com/tseemann/snippy
[00:32:04] Detected operating system: linux
[00:32:04] Enabling bundled linux tools.
[00:32:04] Found bwa - /usr/local/bin/bwa
[00:32:04] Found bcftools - /usr/local/bin/bcftools
[00:32:04] Found samtools - /usr/local/bin/samtools
[00:32:04] Found java - /usr/local/bin/java
[00:32:04] Found snpEff - /usr/local/bin/snpEff
[00:32:04] Found samclip - /usr/local/bin/samclip
[00:32:04] Found seqtk - /usr/local/bin/seqtk
[00:32:04] Found parallel - /usr/local/bin/parallel
[00:32:04] Found freebayes - /usr/local/bin/freebayes
[00:32:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:32:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:32:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:32:04] Found vcfuniq - /usr/local/bin/vcfuniq
[00:32:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:32:04] Found gzip - /bin/gzip
[00:32:04] Found vt - /usr/local/bin/vt
[00:32:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:32:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:32:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:32:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:32:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:32:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:32:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:32:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [01:23:37] This is snippy 4.6.0Show full stderr[01:23:37] This is snippy 4.6.0
[01:23:37] Written by Torsten Seemann
[01:23:37] Obtained from https://github.com/tseemann/snippy
[01:23:37] Detected operating system: linux
[01:23:37] Enabling bundled linux tools.
[01:23:37] Found bwa - /usr/local/bin/bwa
[01:23:37] Found bcftools - /usr/local/bin/bcftools
[01:23:37] Found samtools - /usr/local/bin/samtools
[01:23:37] Found java - /usr/local/bin/java
[01:23:37] Found snpEff - /usr/local/bin/snpEff
[01:23:37] Found samclip - /usr/local/bin/samclip
[01:23:37] Found seqtk - /usr/local/bin/seqtk
[01:23:37] Found parallel - /usr/local/bin/parallel
[01:23:37] Found freebayes - /usr/local/bin/freebayes
[01:23:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:23:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:23:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:23:37] Found vcfuniq - /usr/local/bin/vcfuniq
[01:23:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:23:37] Found gzip - /bin/gzip
[01:23:37] Found vt - /usr/local/bin/vt
[01:23:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:23:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:23:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:23:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:23:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:23:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:23:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:23:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:32:37] This is snippy 4.6.0Show full stderr[00:32:37] This is snippy 4.6.0
[00:32:37] Written by Torsten Seemann
[00:32:37] Obtained from https://github.com/tseemann/snippy
[00:32:37] Detected operating system: linux
[00:32:37] Enabling bundled linux tools.
[00:32:37] Found bwa - /usr/local/bin/bwa
[00:32:37] Found bcftools - /usr/local/bin/bcftools
[00:32:37] Found samtools - /usr/local/bin/samtools
[00:32:37] Found java - /usr/local/bin/java
[00:32:37] Found snpEff - /usr/local/bin/snpEff
[00:32:37] Found samclip - /usr/local/bin/samclip
[00:32:37] Found seqtk - /usr/local/bin/seqtk
[00:32:37] Found parallel - /usr/local/bin/parallel
[00:32:37] Found freebayes - /usr/local/bin/freebayes
[00:32:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:32:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:32:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:32:37] Found vcfuniq - /usr/local/bin/vcfuniq
[00:32:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:32:37] Found gzip - /bin/gzip
[00:32:37] Found vt - /usr/local/bin/vt
[00:32:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:32:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:32:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:32:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:32:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:32:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:32:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:32:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:34:39] This is snippy 4.6.0Show full stderr[00:34:39] This is snippy 4.6.0
[00:34:39] Written by Torsten Seemann
[00:34:39] Obtained from https://github.com/tseemann/snippy
[00:34:39] Detected operating system: linux
[00:34:39] Enabling bundled linux tools.
[00:34:39] Found bwa - /usr/local/bin/bwa
[00:34:39] Found bcftools - /usr/local/bin/bcftools
[00:34:39] Found samtools - /usr/local/bin/samtools
[00:34:39] Found java - /usr/local/bin/java
[00:34:39] Found snpEff - /usr/local/bin/snpEff
[00:34:39] Found samclip - /usr/local/bin/samclip
[00:34:39] Found seqtk - /usr/local/bin/seqtk
[00:34:39] Found parallel - /usr/local/bin/parallel
[00:34:39] Found freebayes - /usr/local/bin/freebayes
[00:34:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:34:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:34:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:34:39] Found vcfuniq - /usr/local/bin/vcfuniq
[00:34:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:34:39] Found gzip - /bin/gzip
[00:34:39] Found vt - /usr/local/bin/vt
[00:34:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:34:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:34:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:34:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:34:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:34:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:34:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:34:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:44:19] This is snippy 4.6.0Show full stderr[00:44:19] This is snippy 4.6.0
[00:44:19] Written by Torsten Seemann
[00:44:19] Obtained from https://github.com/tseemann/snippy
[00:44:19] Detected operating system: linux
[00:44:19] Enabling bundled linux tools.
[00:44:19] Found bwa - /usr/local/bin/bwa
[00:44:19] Found bcftools - /usr/local/bin/bcftools
[00:44:19] Found samtools - /usr/local/bin/samtools
[00:44:19] Found java - /usr/local/bin/java
[00:44:19] Found snpEff - /usr/local/bin/snpEff
[00:44:19] Found samclip - /usr/local/bin/samclip
[00:44:19] Found seqtk - /usr/local/bin/seqtk
[00:44:19] Found parallel - /usr/local/bin/parallel
[00:44:19] Found freebayes - /usr/local/bin/freebayes
[00:44:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:44:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:44:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:44:19] Found vcfuniq - /usr/local/bin/vcfuniq
[00:44:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:44:19] Found gzip - /bin/gzip
[00:44:19] Found vt - /usr/local/bin/vt
[00:44:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:44:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:44:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:44:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:44:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:44:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:44:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:44:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:33:42] This is snippy 4.6.0Show full stderr[00:33:42] This is snippy 4.6.0
[00:33:42] Written by Torsten Seemann
[00:33:42] Obtained from https://github.com/tseemann/snippy
[00:33:42] Detected operating system: linux
[00:33:42] Enabling bundled linux tools.
[00:33:42] Found bwa - /usr/local/bin/bwa
[00:33:42] Found bcftools - /usr/local/bin/bcftools
[00:33:42] Found samtools - /usr/local/bin/samtools
[00:33:42] Found java - /usr/local/bin/java
[00:33:42] Found snpEff - /usr/local/bin/snpEff
[00:33:42] Found samclip - /usr/local/bin/samclip
[00:33:42] Found seqtk - /usr/local/bin/seqtk
[00:33:42] Found parallel - /usr/local/bin/parallel
[00:33:42] Found freebayes - /usr/local/bin/freebayes
[00:33:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:42] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:42] Found gzip - /bin/gzip
[00:33:42] Found vt - /usr/local/bin/vt
[00:33:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:48:20] This is snippy 4.6.0Show full stderr[00:48:20] This is snippy 4.6.0
[00:48:20] Written by Torsten Seemann
[00:48:20] Obtained from https://github.com/tseemann/snippy
[00:48:20] Detected operating system: linux
[00:48:20] Enabling bundled linux tools.
[00:48:20] Found bwa - /usr/local/bin/bwa
[00:48:20] Found bcftools - /usr/local/bin/bcftools
[00:48:20] Found samtools - /usr/local/bin/samtools
[00:48:20] Found java - /usr/local/bin/java
[00:48:20] Found snpEff - /usr/local/bin/snpEff
[00:48:20] Found samclip - /usr/local/bin/samclip
[00:48:20] Found seqtk - /usr/local/bin/seqtk
[00:48:20] Found parallel - /usr/local/bin/parallel
[00:48:20] Found freebayes - /usr/local/bin/freebayes
[00:48:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:48:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:48:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:48:20] Found vcfuniq - /usr/local/bin/vcfuniq
[00:48:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:48:20] Found gzip - /bin/gzip
[00:48:20] Found vt - /usr/local/bin/vt
[00:48:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:48:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:48:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:48:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:48:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:48:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:48:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:48:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:34:03] This is snippy 4.6.0Show full stderr[00:34:03] This is snippy 4.6.0
[00:34:03] Written by Torsten Seemann
[00:34:03] Obtained from https://github.com/tseemann/snippy
[00:34:03] Detected operating system: linux
[00:34:03] Enabling bundled linux tools.
[00:34:03] Found bwa - /usr/local/bin/bwa
[00:34:03] Found bcftools - /usr/local/bin/bcftools
[00:34:03] Found samtools - /usr/local/bin/samtools
[00:34:03] Found java - /usr/local/bin/java
[00:34:03] Found snpEff - /usr/local/bin/snpEff
[00:34:03] Found samclip - /usr/local/bin/samclip
[00:34:03] Found seqtk - /usr/local/bin/seqtk
[00:34:03] Found parallel - /usr/local/bin/parallel
[00:34:03] Found freebayes - /usr/local/bin/freebayes
[00:34:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:34:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:34:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:34:03] Found vcfuniq - /usr/local/bin/vcfuniq
[00:34:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:34:03] Found gzip - /bin/gzip
[00:34:03] Found vt - /usr/local/bin/vt
[00:34:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:34:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:34:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:34:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:34:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:34:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:34:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:34:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [00:34:21] This is snippy 4.6.0Show full stderr[00:34:21] This is snippy 4.6.0
[00:34:21] Written by Torsten Seemann
[00:34:21] Obtained from https://github.com/tseemann/snippy
[00:34:21] Detected operating system: linux
[00:34:21] Enabling bundled linux tools.
[00:34:21] Found bwa - /usr/local/bin/bwa
[00:34:21] Found bcftools - /usr/local/bin/bcftools
[00:34:21] Found samtools - /usr/local/bin/samtools
[00:34:21] Found java - /usr/local/bin/java
[00:34:21] Found snpEff - /usr/local/bin/snpEff
[00:34:21] Found samclip - /usr/local/bin/samclip
[00:34:21] Found seqtk - /usr/local/bin/seqtk
[00:34:21] Found parallel - /usr/local/bin/parallel
[00:34:21] Found freebayes - /usr/local/bin/freebayes
[00:34:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:34:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:34:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:34:21] Found vcfuniq - /usr/local/bin/vcfuniq
[00:34:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:34:21] Found gzip - /bin/gzip
[00:34:21] Found vt - /usr/local/bin/vt
[00:34:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:34:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:34:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:34:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:34:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:34:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:34:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:34:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [01:31:06] This is snippy 4.6.0Show full stderr[01:31:06] This is snippy 4.6.0
[01:31:06] Written by Torsten Seemann
[01:31:06] Obtained from https://github.com/tseemann/snippy
[01:31:06] Detected operating system: linux
[01:31:06] Enabling bundled linux tools.
[01:31:06] Found bwa - /usr/local/bin/bwa
[01:31:06] Found bcftools - /usr/local/bin/bcftools
[01:31:06] Found samtools - /usr/local/bin/samtools
[01:31:06] Found java - /usr/local/bin/java
[01:31:06] Found snpEff - /usr/local/bin/snpEff
[01:31:06] Found samclip - /usr/local/bin/samclip
[01:31:06] Found seqtk - /usr/local/bin/seqtk
[01:31:06] Found parallel - /usr/local/bin/parallel
[01:31:06] Found freebayes - /usr/local/bin/freebayes
[01:31:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:31:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:31:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:31:06] Found vcfuniq - /usr/local/bin/vcfuniq
[01:31:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:31:06] Found gzip - /bin/gzip
[01:31:06] Found vt - /usr/local/bin/vt
[01:31:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:31:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:31:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:31:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:31:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:31:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:31:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:31:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [01:00:22] This is snippy 4.6.0Show full stderr[01:00:22] This is snippy 4.6.0
[01:00:22] Written by Torsten Seemann
[01:00:22] Obtained from https://github.com/tseemann/snippy
[01:00:22] Detected operating system: linux
[01:00:22] Enabling bundled linux tools.
[01:00:22] Found bwa - /usr/local/bin/bwa
[01:00:22] Found bcftools - /usr/local/bin/bcftools
[01:00:22] Found samtools - /usr/local/bin/samtools
[01:00:22] Found java - /usr/local/bin/java
[01:00:22] Found snpEff - /usr/local/bin/snpEff
[01:00:22] Found samclip - /usr/local/bin/samclip
[01:00:22] Found seqtk - /usr/local/bin/seqtk
[01:00:22] Found parallel - /usr/local/bin/parallel
[01:00:22] Found freebayes - /usr/local/bin/freebayes
[01:00:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:00:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:00:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:00:22] Found vcfuniq - /usr/local/bin/vcfuniq
[01:00:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:00:22] Found gzip - /bin/gzip
[01:00:22] Found vt - /usr/local/bin/vt
[01:00:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:00:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:00:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:00:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:00:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:00:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:00:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:00:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [08:55:01] This is snippy 4.6.0Show full stderr[08:55:01] This is snippy 4.6.0
[08:55:01] Written by Torsten Seemann
[08:55:01] Obtained from https://github.com/tseemann/snippy
[08:55:01] Detected operating system: linux
[08:55:01] Enabling bundled linux tools.
[08:55:01] Found bwa - /usr/local/bin/bwa
[08:55:01] Found bcftools - /usr/local/bin/bcftools
[08:55:01] Found samtools - /usr/local/bin/samtools
[08:55:01] Found java - /usr/local/bin/java
[08:55:01] Found snpEff - /usr/local/bin/snpEff
[08:55:01] Found samclip - /usr/local/bin/samclip
[08:55:01] Found seqtk - /usr/local/bin/seqtk
[08:55:01] Found parallel - /usr/local/bin/parallel
[08:55:01] Found freebayes - /usr/local/bin/freebayes
[08:55:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:55:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:55:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:55:01] Found vcfuniq - /usr/local/bin/vcfuniq
[08:55:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:55:01] Found gzip - /bin/gzip
[08:55:01] Found vt - /usr/local/bin/vt
[08:55:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:55:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:55:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:55:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:55:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:55:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:55:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:55:02] Using reference: /corral4/main/objects/7/5/0/dataset_750a1866-e250-4785-864e-3176f0899da8.dat
[08:55:02] Treating reference as 'genbank' format.
[08:55:02] Will use 1 CPU cores.
[08:55:02] Using read file: /corral4/main/objects/0/4/9/dataset_0497b5ba-1d9b-4e33-8e5d-487ce10cf95c.dat
[08:55:02] Creating folder: PAK_resistant_Strain_zip
[08:55:02] Changing working directory: PAK_resistant_Strain_zip
[08:55:02] Creating reference folder: reference
[08:55:02] Extracting FASTA and GFF from reference.
[08:55:05] Wrote 1 sequences to ref.fa
[08:55:05] Wrote 5867 features to ref.gff
[08:55:05] Creating reference/snpeff.config
[08:55:05] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:55:05] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:55:05] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:55:05] Running: bwa index reference/ref.fa 2>> snps.log
[08:55:10] Error running command, check PAK_resistant_Strain_zip/snps.log |
| 2 | [08:56:01] This is snippy 4.6.0Show full stderr[08:56:01] This is snippy 4.6.0
[08:56:01] Written by Torsten Seemann
[08:56:01] Obtained from https://github.com/tseemann/snippy
[08:56:01] Detected operating system: linux
[08:56:01] Enabling bundled linux tools.
[08:56:01] Found bwa - /usr/local/bin/bwa
[08:56:01] Found bcftools - /usr/local/bin/bcftools
[08:56:01] Found samtools - /usr/local/bin/samtools
[08:56:01] Found java - /usr/local/bin/java
[08:56:01] Found snpEff - /usr/local/bin/snpEff
[08:56:01] Found samclip - /usr/local/bin/samclip
[08:56:01] Found seqtk - /usr/local/bin/seqtk
[08:56:01] Found parallel - /usr/local/bin/parallel
[08:56:01] Found freebayes - /usr/local/bin/freebayes
[08:56:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:56:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:56:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:56:01] Found vcfuniq - /usr/local/bin/vcfuniq
[08:56:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:56:01] Found gzip - /bin/gzip
[08:56:01] Found vt - /usr/local/bin/vt
[08:56:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:56:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:56:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:56:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:56:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:56:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:56:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:56:01] Using reference: /corral4/main/objects/4/a/f/dataset_4af21818-52fd-41ed-b756-3780f3f34fd3.dat
[08:56:01] Treating reference as 'genbank' format.
[08:56:01] Will use 1 CPU cores.
[08:56:01] Using read file: /corral4/main/objects/3/1/3/dataset_3133fc9f-f54e-447d-8f0e-2b980a1bc605.dat
[08:56:01] Creating folder: PAK_resistant_Strain_zip
[08:56:01] Changing working directory: PAK_resistant_Strain_zip
[08:56:01] Creating reference folder: reference
[08:56:01] Extracting FASTA and GFF from reference.
[08:56:05] Wrote 1 sequences to ref.fa
[08:56:05] Wrote 5867 features to ref.gff
[08:56:05] Creating reference/snpeff.config
[08:56:05] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:56:05] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:56:05] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:56:05] Running: bwa index reference/ref.fa 2>> snps.log
[08:56:09] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[08:56:09] Running: ln -sf reference/ref.fa . 2>> snps.log
[08:56:09] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[08:56:09] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[08:56:09] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[08:56:15] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/3/1/3/dataset_3133fc9f-f54e-447d-8f0e-2b980a1bc605.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013944/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013944/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013944/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences |
| 2 | [08:58:26] This is snippy 4.6.0Show full stderr[08:58:26] This is snippy 4.6.0
[08:58:26] Written by Torsten Seemann
[08:58:26] Obtained from https://github.com/tseemann/snippy
[08:58:26] Detected operating system: linux
[08:58:26] Enabling bundled linux tools.
[08:58:26] Found bwa - /usr/local/bin/bwa
[08:58:26] Found bcftools - /usr/local/bin/bcftools
[08:58:26] Found samtools - /usr/local/bin/samtools
[08:58:26] Found java - /usr/local/bin/java
[08:58:26] Found snpEff - /usr/local/bin/snpEff
[08:58:26] Found samclip - /usr/local/bin/samclip
[08:58:26] Found seqtk - /usr/local/bin/seqtk
[08:58:26] Found parallel - /usr/local/bin/parallel
[08:58:26] Found freebayes - /usr/local/bin/freebayes
[08:58:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:58:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:58:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:58:26] Found vcfuniq - /usr/local/bin/vcfuniq
[08:58:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:58:26] Found gzip - /bin/gzip
[08:58:26] Found vt - /usr/local/bin/vt
[08:58:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:58:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:58:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:58:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:58:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:58:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:58:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:58:27] Using reference: /corral4/main/objects/7/e/4/dataset_7e4b9f0c-299c-4b3c-a179-d1102993c678.dat
[08:58:27] Treating reference as 'genbank' format.
[08:58:27] Will use 1 CPU cores.
[08:58:27] Using read file: /corral4/main/objects/1/8/8/dataset_18865a20-ae2d-4536-9508-ef198472e7e4.dat
[08:58:27] Creating folder: PAK_resistant_Strain_zip
[08:58:27] Changing working directory: PAK_resistant_Strain_zip
[08:58:27] Creating reference folder: reference
[08:58:27] Extracting FASTA and GFF from reference.
[08:58:30] Wrote 1 sequences to ref.fa
[08:58:30] Wrote 5867 features to ref.gff
[08:58:30] Creating reference/snpeff.config
[08:58:31] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[08:58:31] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:58:31] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:58:31] Error running command, check PAK_resistant_Strain_zip/snps.log |
| 2 | [21:22:23] This is snippy 4.6.0Show full stderr[21:22:23] This is snippy 4.6.0
[21:22:23] Written by Torsten Seemann
[21:22:23] Obtained from https://github.com/tseemann/snippy
[21:22:23] Detected operating system: linux
[21:22:23] Enabling bundled linux tools.
[21:22:23] Found bwa - /usr/local/bin/bwa
[21:22:23] Found bcftools - /usr/local/bin/bcftools
[21:22:23] Found samtools - /usr/local/bin/samtools
[21:22:23] Found java - /usr/local/bin/java
[21:22:23] Found snpEff - /usr/local/bin/snpEff
[21:22:23] Found samclip - /usr/local/bin/samclip
[21:22:23] Found seqtk - /usr/local/bin/seqtk
[21:22:23] Found parallel - /usr/local/bin/parallel
[21:22:23] Found freebayes - /usr/local/bin/freebayes
[21:22:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:22:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:22:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:22:23] Found vcfuniq - /usr/local/bin/vcfuniq
[21:22:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:22:23] Found gzip - /bin/gzip
[21:22:23] Found vt - /usr/local/bin/vt
[21:22:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:22:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:22:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:22:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:22:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:22:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:22:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:22:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [21:22:16] This is snippy 4.6.0Show full stderr[21:22:16] This is snippy 4.6.0
[21:22:16] Written by Torsten Seemann
[21:22:16] Obtained from https://github.com/tseemann/snippy
[21:22:16] Detected operating system: linux
[21:22:16] Enabling bundled linux tools.
[21:22:16] Found bwa - /usr/local/bin/bwa
[21:22:16] Found bcftools - /usr/local/bin/bcftools
[21:22:16] Found samtools - /usr/local/bin/samtools
[21:22:16] Found java - /usr/local/bin/java
[21:22:16] Found snpEff - /usr/local/bin/snpEff
[21:22:16] Found samclip - /usr/local/bin/samclip
[21:22:16] Found seqtk - /usr/local/bin/seqtk
[21:22:16] Found parallel - /usr/local/bin/parallel
[21:22:16] Found freebayes - /usr/local/bin/freebayes
[21:22:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:22:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:22:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:22:16] Found vcfuniq - /usr/local/bin/vcfuniq
[21:22:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:22:16] Found gzip - /bin/gzip
[21:22:16] Found vt - /usr/local/bin/vt
[21:22:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:22:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:22:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:22:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:22:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:22:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:22:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:22:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [21:27:46] This is snippy 4.6.0Show full stderr[21:27:46] This is snippy 4.6.0
[21:27:46] Written by Torsten Seemann
[21:27:46] Obtained from https://github.com/tseemann/snippy
[21:27:46] Detected operating system: linux
[21:27:46] Enabling bundled linux tools.
[21:27:46] Found bwa - /usr/local/bin/bwa
[21:27:46] Found bcftools - /usr/local/bin/bcftools
[21:27:46] Found samtools - /usr/local/bin/samtools
[21:27:46] Found java - /usr/local/bin/java
[21:27:46] Found snpEff - /usr/local/bin/snpEff
[21:27:46] Found samclip - /usr/local/bin/samclip
[21:27:46] Found seqtk - /usr/local/bin/seqtk
[21:27:46] Found parallel - /usr/local/bin/parallel
[21:27:46] Found freebayes - /usr/local/bin/freebayes
[21:27:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:27:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:27:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:27:46] Found vcfuniq - /usr/local/bin/vcfuniq
[21:27:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:27:46] Found gzip - /bin/gzip
[21:27:46] Found vt - /usr/local/bin/vt
[21:27:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:27:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:27:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:27:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:27:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:27:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:27:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:27:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:57:18] This is snippy 4.6.0Show full stderr[05:57:18] This is snippy 4.6.0
[05:57:18] Written by Torsten Seemann
[05:57:18] Obtained from https://github.com/tseemann/snippy
[05:57:18] Detected operating system: linux
[05:57:18] Enabling bundled linux tools.
[05:57:18] Found bwa - /usr/local/bin/bwa
[05:57:18] Found bcftools - /usr/local/bin/bcftools
[05:57:18] Found samtools - /usr/local/bin/samtools
[05:57:18] Found java - /usr/local/bin/java
[05:57:18] Found snpEff - /usr/local/bin/snpEff
[05:57:18] Found samclip - /usr/local/bin/samclip
[05:57:18] Found seqtk - /usr/local/bin/seqtk
[05:57:18] Found parallel - /usr/local/bin/parallel
[05:57:18] Found freebayes - /usr/local/bin/freebayes
[05:57:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:57:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:57:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:57:18] Found vcfuniq - /usr/local/bin/vcfuniq
[05:57:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:57:18] Found gzip - /bin/gzip
[05:57:18] Found vt - /usr/local/bin/vt
[05:57:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:57:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:57:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:57:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:57:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:57:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:57:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:57:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 2 | [05:57:17] This is snippy 4.6.0Show full stderr[05:57:17] This is snippy 4.6.0
[05:57:17] Written by Torsten Seemann
[05:57:17] Obtained from https://github.com/tseemann/snippy
[05:57:17] Detected operating system: linux
[05:57:17] Enabling bundled linux tools.
[05:57:17] Found bwa - /usr/local/bin/bwa
[05:57:17] Found bcftools - /usr/local/bin/bcftools
[05:57:17] Found samtools - /usr/local/bin/samtools
[05:57:17] Found java - /usr/local/bin/java
[05:57:17] Found snpEff - /usr/local/bin/snpEff
[05:57:17] Found samclip - /usr/local/bin/samclip
[05:57:17] Found seqtk - /usr/local/bin/seqtk
[05:57:17] Found parallel - /usr/local/bin/parallel
[05:57:17] Found freebayes - /usr/local/bin/freebayes
[05:57:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:57:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:57:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:57:17] Found vcfuniq - /usr/local/bin/vcfuniq
[05:57:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:57:17] Found gzip - /bin/gzip
[05:57:17] Found vt - /usr/local/bin/vt
[05:57:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:57:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:57:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:57:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:57:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:57:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:57:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:57:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:24:12] This is snippy 4.6.0Show full stderr[21:24:12] This is snippy 4.6.0
[21:24:12] Written by Torsten Seemann
[21:24:12] Obtained from https://github.com/tseemann/snippy
[21:24:12] Detected operating system: linux
[21:24:12] Enabling bundled linux tools.
[21:24:12] Found bwa - /usr/local/bin/bwa
[21:24:12] Found bcftools - /usr/local/bin/bcftools
[21:24:12] Found samtools - /usr/local/bin/samtools
[21:24:12] Found java - /usr/local/bin/java
[21:24:12] Found snpEff - /usr/local/bin/snpEff
[21:24:12] Found samclip - /usr/local/bin/samclip
[21:24:12] Found seqtk - /usr/local/bin/seqtk
[21:24:12] Found parallel - /usr/local/bin/parallel
[21:24:12] Found freebayes - /usr/local/bin/freebayes
[21:24:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:24:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:24:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:24:12] Found vcfuniq - /usr/local/bin/vcfuniq
[21:24:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:24:12] Found gzip - /bin/gzip
[21:24:12] Found vt - /usr/local/bin/vt
[21:24:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:24:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:24:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:24:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:24:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:24:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:24:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:24:13] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:24:13] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:24:15] This is snippy 4.6.0Show full stderr[21:24:15] This is snippy 4.6.0
[21:24:15] Written by Torsten Seemann
[21:24:15] Obtained from https://github.com/tseemann/snippy
[21:24:15] Detected operating system: linux
[21:24:15] Enabling bundled linux tools.
[21:24:15] Found bwa - /usr/local/bin/bwa
[21:24:15] Found bcftools - /usr/local/bin/bcftools
[21:24:15] Found samtools - /usr/local/bin/samtools
[21:24:15] Found java - /usr/local/bin/java
[21:24:15] Found snpEff - /usr/local/bin/snpEff
[21:24:15] Found samclip - /usr/local/bin/samclip
[21:24:15] Found seqtk - /usr/local/bin/seqtk
[21:24:15] Found parallel - /usr/local/bin/parallel
[21:24:15] Found freebayes - /usr/local/bin/freebayes
[21:24:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:24:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:24:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:24:15] Found vcfuniq - /usr/local/bin/vcfuniq
[21:24:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:24:15] Found gzip - /bin/gzip
[21:24:15] Found vt - /usr/local/bin/vt
[21:24:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:24:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:24:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:24:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:24:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:24:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:24:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:24:17] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:24:17] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:24:19] This is snippy 4.6.0Show full stderr[21:24:19] This is snippy 4.6.0
[21:24:19] Written by Torsten Seemann
[21:24:19] Obtained from https://github.com/tseemann/snippy
[21:24:19] Detected operating system: linux
[21:24:19] Enabling bundled linux tools.
[21:24:19] Found bwa - /usr/local/bin/bwa
[21:24:19] Found bcftools - /usr/local/bin/bcftools
[21:24:19] Found samtools - /usr/local/bin/samtools
[21:24:19] Found java - /usr/local/bin/java
[21:24:19] Found snpEff - /usr/local/bin/snpEff
[21:24:19] Found samclip - /usr/local/bin/samclip
[21:24:19] Found seqtk - /usr/local/bin/seqtk
[21:24:19] Found parallel - /usr/local/bin/parallel
[21:24:19] Found freebayes - /usr/local/bin/freebayes
[21:24:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:24:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:24:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:24:19] Found vcfuniq - /usr/local/bin/vcfuniq
[21:24:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:24:19] Found gzip - /bin/gzip
[21:24:19] Found vt - /usr/local/bin/vt
[21:24:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:24:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:24:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:24:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:24:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:24:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:24:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:24:20] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:24:20] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:24:17] This is snippy 4.6.0Show full stderr[21:24:17] This is snippy 4.6.0
[21:24:17] Written by Torsten Seemann
[21:24:17] Obtained from https://github.com/tseemann/snippy
[21:24:17] Detected operating system: linux
[21:24:17] Enabling bundled linux tools.
[21:24:17] Found bwa - /usr/local/bin/bwa
[21:24:17] Found bcftools - /usr/local/bin/bcftools
[21:24:17] Found samtools - /usr/local/bin/samtools
[21:24:17] Found java - /usr/local/bin/java
[21:24:17] Found snpEff - /usr/local/bin/snpEff
[21:24:17] Found samclip - /usr/local/bin/samclip
[21:24:17] Found seqtk - /usr/local/bin/seqtk
[21:24:17] Found parallel - /usr/local/bin/parallel
[21:24:17] Found freebayes - /usr/local/bin/freebayes
[21:24:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:24:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:24:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:24:17] Found vcfuniq - /usr/local/bin/vcfuniq
[21:24:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:24:17] Found gzip - /bin/gzip
[21:24:17] Found vt - /usr/local/bin/vt
[21:24:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:24:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:24:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:24:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:24:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:24:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:24:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:24:18] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:24:18] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:24:30] This is snippy 4.6.0Show full stderr[21:24:30] This is snippy 4.6.0
[21:24:30] Written by Torsten Seemann
[21:24:30] Obtained from https://github.com/tseemann/snippy
[21:24:30] Detected operating system: linux
[21:24:30] Enabling bundled linux tools.
[21:24:30] Found bwa - /usr/local/bin/bwa
[21:24:30] Found bcftools - /usr/local/bin/bcftools
[21:24:30] Found samtools - /usr/local/bin/samtools
[21:24:30] Found java - /usr/local/bin/java
[21:24:30] Found snpEff - /usr/local/bin/snpEff
[21:24:30] Found samclip - /usr/local/bin/samclip
[21:24:30] Found seqtk - /usr/local/bin/seqtk
[21:24:30] Found parallel - /usr/local/bin/parallel
[21:24:30] Found freebayes - /usr/local/bin/freebayes
[21:24:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:24:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:24:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:24:30] Found vcfuniq - /usr/local/bin/vcfuniq
[21:24:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:24:30] Found gzip - /bin/gzip
[21:24:30] Found vt - /usr/local/bin/vt
[21:24:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:24:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:24:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:24:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:24:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:24:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:24:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:24:31] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:24:31] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:24:32] This is snippy 4.6.0Show full stderr[21:24:32] This is snippy 4.6.0
[21:24:32] Written by Torsten Seemann
[21:24:32] Obtained from https://github.com/tseemann/snippy
[21:24:32] Detected operating system: linux
[21:24:32] Enabling bundled linux tools.
[21:24:32] Found bwa - /usr/local/bin/bwa
[21:24:32] Found bcftools - /usr/local/bin/bcftools
[21:24:32] Found samtools - /usr/local/bin/samtools
[21:24:32] Found java - /usr/local/bin/java
[21:24:32] Found snpEff - /usr/local/bin/snpEff
[21:24:32] Found samclip - /usr/local/bin/samclip
[21:24:32] Found seqtk - /usr/local/bin/seqtk
[21:24:32] Found parallel - /usr/local/bin/parallel
[21:24:32] Found freebayes - /usr/local/bin/freebayes
[21:24:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:24:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:24:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:24:32] Found vcfuniq - /usr/local/bin/vcfuniq
[21:24:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:24:32] Found gzip - /bin/gzip
[21:24:32] Found vt - /usr/local/bin/vt
[21:24:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:24:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:24:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:24:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:24:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:24:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:24:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:24:33] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:24:33] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:25:05] This is snippy 4.6.0Show full stderr[21:25:05] This is snippy 4.6.0
[21:25:05] Written by Torsten Seemann
[21:25:05] Obtained from https://github.com/tseemann/snippy
[21:25:05] Detected operating system: linux
[21:25:05] Enabling bundled linux tools.
[21:25:05] Found bwa - /usr/local/bin/bwa
[21:25:05] Found bcftools - /usr/local/bin/bcftools
[21:25:05] Found samtools - /usr/local/bin/samtools
[21:25:05] Found java - /usr/local/bin/java
[21:25:05] Found snpEff - /usr/local/bin/snpEff
[21:25:05] Found samclip - /usr/local/bin/samclip
[21:25:05] Found seqtk - /usr/local/bin/seqtk
[21:25:05] Found parallel - /usr/local/bin/parallel
[21:25:05] Found freebayes - /usr/local/bin/freebayes
[21:25:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:25:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:25:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:25:05] Found vcfuniq - /usr/local/bin/vcfuniq
[21:25:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:25:05] Found gzip - /bin/gzip
[21:25:05] Found vt - /usr/local/bin/vt
[21:25:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:25:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:25:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:25:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:25:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:25:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:25:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:25:06] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:25:07] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:25:08] This is snippy 4.6.0Show full stderr[21:25:08] This is snippy 4.6.0
[21:25:08] Written by Torsten Seemann
[21:25:08] Obtained from https://github.com/tseemann/snippy
[21:25:08] Detected operating system: linux
[21:25:08] Enabling bundled linux tools.
[21:25:08] Found bwa - /usr/local/bin/bwa
[21:25:08] Found bcftools - /usr/local/bin/bcftools
[21:25:08] Found samtools - /usr/local/bin/samtools
[21:25:08] Found java - /usr/local/bin/java
[21:25:08] Found snpEff - /usr/local/bin/snpEff
[21:25:08] Found samclip - /usr/local/bin/samclip
[21:25:08] Found seqtk - /usr/local/bin/seqtk
[21:25:08] Found parallel - /usr/local/bin/parallel
[21:25:08] Found freebayes - /usr/local/bin/freebayes
[21:25:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:25:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:25:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:25:08] Found vcfuniq - /usr/local/bin/vcfuniq
[21:25:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:25:08] Found gzip - /bin/gzip
[21:25:08] Found vt - /usr/local/bin/vt
[21:25:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:25:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:25:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:25:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:25:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:25:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:25:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:25:09] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:25:09] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:34:14] This is snippy 4.6.0Show full stderr[21:34:14] This is snippy 4.6.0
[21:34:14] Written by Torsten Seemann
[21:34:14] Obtained from https://github.com/tseemann/snippy
[21:34:14] Detected operating system: linux
[21:34:14] Enabling bundled linux tools.
[21:34:14] Found bwa - /usr/local/bin/bwa
[21:34:14] Found bcftools - /usr/local/bin/bcftools
[21:34:14] Found samtools - /usr/local/bin/samtools
[21:34:14] Found java - /usr/local/bin/java
[21:34:14] Found snpEff - /usr/local/bin/snpEff
[21:34:14] Found samclip - /usr/local/bin/samclip
[21:34:14] Found seqtk - /usr/local/bin/seqtk
[21:34:14] Found parallel - /usr/local/bin/parallel
[21:34:14] Found freebayes - /usr/local/bin/freebayes
[21:34:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:34:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:34:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:34:14] Found vcfuniq - /usr/local/bin/vcfuniq
[21:34:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:34:14] Found gzip - /bin/gzip
[21:34:14] Found vt - /usr/local/bin/vt
[21:34:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:34:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:34:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:34:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:34:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:34:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:34:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:34:15] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:34:15] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:34:34] This is snippy 4.6.0Show full stderr[21:34:34] This is snippy 4.6.0
[21:34:34] Written by Torsten Seemann
[21:34:34] Obtained from https://github.com/tseemann/snippy
[21:34:34] Detected operating system: linux
[21:34:34] Enabling bundled linux tools.
[21:34:34] Found bwa - /usr/local/bin/bwa
[21:34:34] Found bcftools - /usr/local/bin/bcftools
[21:34:34] Found samtools - /usr/local/bin/samtools
[21:34:34] Found java - /usr/local/bin/java
[21:34:34] Found snpEff - /usr/local/bin/snpEff
[21:34:34] Found samclip - /usr/local/bin/samclip
[21:34:34] Found seqtk - /usr/local/bin/seqtk
[21:34:34] Found parallel - /usr/local/bin/parallel
[21:34:34] Found freebayes - /usr/local/bin/freebayes
[21:34:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:34:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:34:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:34:34] Found vcfuniq - /usr/local/bin/vcfuniq
[21:34:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:34:34] Found gzip - /bin/gzip
[21:34:34] Found vt - /usr/local/bin/vt
[21:34:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:34:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:34:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:34:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:34:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:34:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:34:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:34:35] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:34:35] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:34:59] This is snippy 4.6.0Show full stderr[21:34:59] This is snippy 4.6.0
[21:34:59] Written by Torsten Seemann
[21:34:59] Obtained from https://github.com/tseemann/snippy
[21:34:59] Detected operating system: linux
[21:34:59] Enabling bundled linux tools.
[21:34:59] Found bwa - /usr/local/bin/bwa
[21:34:59] Found bcftools - /usr/local/bin/bcftools
[21:34:59] Found samtools - /usr/local/bin/samtools
[21:34:59] Found java - /usr/local/bin/java
[21:34:59] Found snpEff - /usr/local/bin/snpEff
[21:34:59] Found samclip - /usr/local/bin/samclip
[21:34:59] Found seqtk - /usr/local/bin/seqtk
[21:34:59] Found parallel - /usr/local/bin/parallel
[21:34:59] Found freebayes - /usr/local/bin/freebayes
[21:34:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:34:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:34:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:34:59] Found vcfuniq - /usr/local/bin/vcfuniq
[21:34:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:34:59] Found gzip - /bin/gzip
[21:34:59] Found vt - /usr/local/bin/vt
[21:34:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:34:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:34:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:34:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:34:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:35:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:35:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:35:00] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:35:00] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:35:00] This is snippy 4.6.0Show full stderr[21:35:00] This is snippy 4.6.0
[21:35:00] Written by Torsten Seemann
[21:35:00] Obtained from https://github.com/tseemann/snippy
[21:35:00] Detected operating system: linux
[21:35:00] Enabling bundled linux tools.
[21:35:00] Found bwa - /usr/local/bin/bwa
[21:35:00] Found bcftools - /usr/local/bin/bcftools
[21:35:00] Found samtools - /usr/local/bin/samtools
[21:35:00] Found java - /usr/local/bin/java
[21:35:00] Found snpEff - /usr/local/bin/snpEff
[21:35:00] Found samclip - /usr/local/bin/samclip
[21:35:00] Found seqtk - /usr/local/bin/seqtk
[21:35:00] Found parallel - /usr/local/bin/parallel
[21:35:00] Found freebayes - /usr/local/bin/freebayes
[21:35:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:35:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:35:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:35:00] Found vcfuniq - /usr/local/bin/vcfuniq
[21:35:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:35:00] Found gzip - /bin/gzip
[21:35:00] Found vt - /usr/local/bin/vt
[21:35:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:35:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:35:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:35:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:35:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:35:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:35:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:35:01] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:35:01] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:35:14] This is snippy 4.6.0Show full stderr[21:35:14] This is snippy 4.6.0
[21:35:14] Written by Torsten Seemann
[21:35:14] Obtained from https://github.com/tseemann/snippy
[21:35:14] Detected operating system: linux
[21:35:14] Enabling bundled linux tools.
[21:35:14] Found bwa - /usr/local/bin/bwa
[21:35:14] Found bcftools - /usr/local/bin/bcftools
[21:35:14] Found samtools - /usr/local/bin/samtools
[21:35:14] Found java - /usr/local/bin/java
[21:35:14] Found snpEff - /usr/local/bin/snpEff
[21:35:14] Found samclip - /usr/local/bin/samclip
[21:35:14] Found seqtk - /usr/local/bin/seqtk
[21:35:14] Found parallel - /usr/local/bin/parallel
[21:35:14] Found freebayes - /usr/local/bin/freebayes
[21:35:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:35:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:35:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:35:14] Found vcfuniq - /usr/local/bin/vcfuniq
[21:35:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:35:14] Found gzip - /bin/gzip
[21:35:14] Found vt - /usr/local/bin/vt
[21:35:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:35:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:35:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:35:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:35:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:35:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:35:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:35:15] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:35:15] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:35:17] This is snippy 4.6.0Show full stderr[21:35:17] This is snippy 4.6.0
[21:35:17] Written by Torsten Seemann
[21:35:17] Obtained from https://github.com/tseemann/snippy
[21:35:17] Detected operating system: linux
[21:35:17] Enabling bundled linux tools.
[21:35:17] Found bwa - /usr/local/bin/bwa
[21:35:17] Found bcftools - /usr/local/bin/bcftools
[21:35:17] Found samtools - /usr/local/bin/samtools
[21:35:17] Found java - /usr/local/bin/java
[21:35:17] Found snpEff - /usr/local/bin/snpEff
[21:35:17] Found samclip - /usr/local/bin/samclip
[21:35:17] Found seqtk - /usr/local/bin/seqtk
[21:35:17] Found parallel - /usr/local/bin/parallel
[21:35:17] Found freebayes - /usr/local/bin/freebayes
[21:35:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:35:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:35:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:35:17] Found vcfuniq - /usr/local/bin/vcfuniq
[21:35:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:35:17] Found gzip - /bin/gzip
[21:35:17] Found vt - /usr/local/bin/vt
[21:35:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:35:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:35:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:35:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:35:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:35:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:35:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:35:18] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:35:18] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:35:20] This is snippy 4.6.0Show full stderr[21:35:20] This is snippy 4.6.0
[21:35:20] Written by Torsten Seemann
[21:35:20] Obtained from https://github.com/tseemann/snippy
[21:35:20] Detected operating system: linux
[21:35:20] Enabling bundled linux tools.
[21:35:20] Found bwa - /usr/local/bin/bwa
[21:35:20] Found bcftools - /usr/local/bin/bcftools
[21:35:20] Found samtools - /usr/local/bin/samtools
[21:35:20] Found java - /usr/local/bin/java
[21:35:20] Found snpEff - /usr/local/bin/snpEff
[21:35:20] Found samclip - /usr/local/bin/samclip
[21:35:20] Found seqtk - /usr/local/bin/seqtk
[21:35:20] Found parallel - /usr/local/bin/parallel
[21:35:20] Found freebayes - /usr/local/bin/freebayes
[21:35:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:35:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:35:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:35:20] Found vcfuniq - /usr/local/bin/vcfuniq
[21:35:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:35:20] Found gzip - /bin/gzip
[21:35:20] Found vt - /usr/local/bin/vt
[21:35:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:35:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:35:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:35:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:35:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:35:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:35:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:35:21] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:35:21] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:34:46] This is snippy 4.6.0Show full stderr[21:34:46] This is snippy 4.6.0
[21:34:46] Written by Torsten Seemann
[21:34:46] Obtained from https://github.com/tseemann/snippy
[21:34:46] Detected operating system: linux
[21:34:46] Enabling bundled linux tools.
[21:34:46] Found bwa - /usr/local/bin/bwa
[21:34:46] Found bcftools - /usr/local/bin/bcftools
[21:34:46] Found samtools - /usr/local/bin/samtools
[21:34:46] Found java - /usr/local/bin/java
[21:34:46] Found snpEff - /usr/local/bin/snpEff
[21:34:46] Found samclip - /usr/local/bin/samclip
[21:34:46] Found seqtk - /usr/local/bin/seqtk
[21:34:46] Found parallel - /usr/local/bin/parallel
[21:34:46] Found freebayes - /usr/local/bin/freebayes
[21:34:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:34:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:34:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:34:46] Found vcfuniq - /usr/local/bin/vcfuniq
[21:34:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:34:46] Found gzip - /bin/gzip
[21:34:46] Found vt - /usr/local/bin/vt
[21:34:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:34:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:34:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:34:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:34:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:34:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:34:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:34:47] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:34:47] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:34:56] This is snippy 4.6.0Show full stderr[21:34:56] This is snippy 4.6.0
[21:34:56] Written by Torsten Seemann
[21:34:56] Obtained from https://github.com/tseemann/snippy
[21:34:56] Detected operating system: linux
[21:34:56] Enabling bundled linux tools.
[21:34:56] Found bwa - /usr/local/bin/bwa
[21:34:56] Found bcftools - /usr/local/bin/bcftools
[21:34:56] Found samtools - /usr/local/bin/samtools
[21:34:57] Found java - /usr/local/bin/java
[21:34:57] Found snpEff - /usr/local/bin/snpEff
[21:34:57] Found samclip - /usr/local/bin/samclip
[21:34:57] Found seqtk - /usr/local/bin/seqtk
[21:34:57] Found parallel - /usr/local/bin/parallel
[21:34:57] Found freebayes - /usr/local/bin/freebayes
[21:34:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:34:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:34:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:34:57] Found vcfuniq - /usr/local/bin/vcfuniq
[21:34:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:34:57] Found gzip - /bin/gzip
[21:34:57] Found vt - /usr/local/bin/vt
[21:34:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:34:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:34:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:34:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:34:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:34:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:34:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:34:58] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:34:58] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:35:02] This is snippy 4.6.0Show full stderr[21:35:02] This is snippy 4.6.0
[21:35:02] Written by Torsten Seemann
[21:35:02] Obtained from https://github.com/tseemann/snippy
[21:35:02] Detected operating system: linux
[21:35:02] Enabling bundled linux tools.
[21:35:02] Found bwa - /usr/local/bin/bwa
[21:35:02] Found bcftools - /usr/local/bin/bcftools
[21:35:02] Found samtools - /usr/local/bin/samtools
[21:35:02] Found java - /usr/local/bin/java
[21:35:02] Found snpEff - /usr/local/bin/snpEff
[21:35:02] Found samclip - /usr/local/bin/samclip
[21:35:02] Found seqtk - /usr/local/bin/seqtk
[21:35:02] Found parallel - /usr/local/bin/parallel
[21:35:02] Found freebayes - /usr/local/bin/freebayes
[21:35:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:35:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:35:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:35:02] Found vcfuniq - /usr/local/bin/vcfuniq
[21:35:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:35:02] Found gzip - /bin/gzip
[21:35:02] Found vt - /usr/local/bin/vt
[21:35:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:35:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:35:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:35:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:35:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:35:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:35:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:35:03] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:35:03] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:35:23] This is snippy 4.6.0Show full stderr[21:35:23] This is snippy 4.6.0
[21:35:23] Written by Torsten Seemann
[21:35:23] Obtained from https://github.com/tseemann/snippy
[21:35:23] Detected operating system: linux
[21:35:23] Enabling bundled linux tools.
[21:35:23] Found bwa - /usr/local/bin/bwa
[21:35:23] Found bcftools - /usr/local/bin/bcftools
[21:35:23] Found samtools - /usr/local/bin/samtools
[21:35:23] Found java - /usr/local/bin/java
[21:35:23] Found snpEff - /usr/local/bin/snpEff
[21:35:23] Found samclip - /usr/local/bin/samclip
[21:35:23] Found seqtk - /usr/local/bin/seqtk
[21:35:23] Found parallel - /usr/local/bin/parallel
[21:35:23] Found freebayes - /usr/local/bin/freebayes
[21:35:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:35:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:35:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:35:23] Found vcfuniq - /usr/local/bin/vcfuniq
[21:35:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:35:24] Found gzip - /bin/gzip
[21:35:24] Found vt - /usr/local/bin/vt
[21:35:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:35:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:35:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:35:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:35:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:35:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:35:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:35:25] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:35:25] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:35:32] This is snippy 4.6.0Show full stderr[21:35:32] This is snippy 4.6.0
[21:35:32] Written by Torsten Seemann
[21:35:32] Obtained from https://github.com/tseemann/snippy
[21:35:32] Detected operating system: linux
[21:35:32] Enabling bundled linux tools.
[21:35:32] Found bwa - /usr/local/bin/bwa
[21:35:32] Found bcftools - /usr/local/bin/bcftools
[21:35:32] Found samtools - /usr/local/bin/samtools
[21:35:32] Found java - /usr/local/bin/java
[21:35:32] Found snpEff - /usr/local/bin/snpEff
[21:35:32] Found samclip - /usr/local/bin/samclip
[21:35:32] Found seqtk - /usr/local/bin/seqtk
[21:35:32] Found parallel - /usr/local/bin/parallel
[21:35:32] Found freebayes - /usr/local/bin/freebayes
[21:35:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:35:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:35:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:35:32] Found vcfuniq - /usr/local/bin/vcfuniq
[21:35:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:35:32] Found gzip - /bin/gzip
[21:35:32] Found vt - /usr/local/bin/vt
[21:35:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:35:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:35:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:35:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:35:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:35:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:35:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:35:33] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:35:33] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [21:35:33] This is snippy 4.6.0Show full stderr[21:35:33] This is snippy 4.6.0
[21:35:33] Written by Torsten Seemann
[21:35:33] Obtained from https://github.com/tseemann/snippy
[21:35:33] Detected operating system: linux
[21:35:33] Enabling bundled linux tools.
[21:35:33] Found bwa - /usr/local/bin/bwa
[21:35:33] Found bcftools - /usr/local/bin/bcftools
[21:35:33] Found samtools - /usr/local/bin/samtools
[21:35:33] Found java - /usr/local/bin/java
[21:35:33] Found snpEff - /usr/local/bin/snpEff
[21:35:33] Found samclip - /usr/local/bin/samclip
[21:35:33] Found seqtk - /usr/local/bin/seqtk
[21:35:33] Found parallel - /usr/local/bin/parallel
[21:35:33] Found freebayes - /usr/local/bin/freebayes
[21:35:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:35:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:35:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:35:33] Found vcfuniq - /usr/local/bin/vcfuniq
[21:35:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:35:33] Found gzip - /bin/gzip
[21:35:33] Found vt - /usr/local/bin/vt
[21:35:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:35:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:35:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:35:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:35:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:35:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:35:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:35:34] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat
[21:35:34] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat' |
| 1 | [22:05:20] This is snippy 4.6.0Show full stderr[22:05:20] This is snippy 4.6.0
[22:05:20] Written by Torsten Seemann
[22:05:20] Obtained from https://github.com/tseemann/snippy
[22:05:20] Detected operating system: linux
[22:05:20] Enabling bundled linux tools.
[22:05:20] Found bwa - /usr/local/bin/bwa
[22:05:20] Found bcftools - /usr/local/bin/bcftools
[22:05:20] Found samtools - /usr/local/bin/samtools
[22:05:20] Found java - /usr/local/bin/java
[22:05:20] Found snpEff - /usr/local/bin/snpEff
[22:05:20] Found samclip - /usr/local/bin/samclip
[22:05:20] Found seqtk - /usr/local/bin/seqtk
[22:05:20] Found parallel - /usr/local/bin/parallel
[22:05:20] Found freebayes - /usr/local/bin/freebayes
[22:05:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:05:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:05:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:05:20] Found vcfuniq - /usr/local/bin/vcfuniq
[22:05:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:05:20] Found gzip - /bin/gzip
[22:05:20] Found vt - /usr/local/bin/vt
[22:05:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:05:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:05:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:05:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:05:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:05:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:05:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:05:21] Using reference: /jetstream2/scratch/main/jobs/72172731/inputs/dataset_c3278295-0534-4341-a983-519e27d93d98.dat
[22:05:21] Treating reference as 'fasta' format.
[22:05:21] Will use 1 CPU cores.
[22:05:21] Using read file: /jetstream2/scratch/main/jobs/72172731/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat
[22:05:21] Creating folder: Select_on_dataset_11
[22:05:21] Changing working directory: Select_on_dataset_11
[22:05:21] Creating reference folder: reference
[22:05:21] Extracting FASTA and GFF from reference.
[22:05:21] Wrote 1 sequences to ref.fa
[22:05:21] Wrote 0 features to ref.gff
[22:05:21] Freebayes will process 1 chunks of 12416664 bp, 1 chunks at a time.
[22:05:21] Using BAM RG (Read Group) ID: Select_on_dataset_11
[22:05:21] Running: samtools faidx reference/ref.fa 2>> snps.log
[22:05:21] Running: bwa index reference/ref.fa 2>> snps.log
[22:05:25] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[22:05:25] Running: ln -sf reference/ref.fa . 2>> snps.log
[22:05:25] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[22:05:25] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[22:05:25] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_11\tSM:Select_on_dataset_11' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72172731/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72172731/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72172731/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72172731/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] Found 1 sequences in reference/ref.fa.fai
[M::process] read 1 sequences (11639536 bp)...
[samclip] Total SAM records 0 |
| 1 | [23:56:35] This is snippy 4.6.0Show full stderr[23:56:35] This is snippy 4.6.0
[23:56:35] Written by Torsten Seemann
[23:56:35] Obtained from https://github.com/tseemann/snippy
[23:56:35] Detected operating system: linux
[23:56:35] Enabling bundled linux tools.
[23:56:35] Found bwa - /usr/local/bin/bwa
[23:56:35] Found bcftools - /usr/local/bin/bcftools
[23:56:35] Found samtools - /usr/local/bin/samtools
[23:56:35] Found java - /usr/local/bin/java
[23:56:35] Found snpEff - /usr/local/bin/snpEff
[23:56:35] Found samclip - /usr/local/bin/samclip
[23:56:35] Found seqtk - /usr/local/bin/seqtk
[23:56:35] Found parallel - /usr/local/bin/parallel
[23:56:35] Found freebayes - /usr/local/bin/freebayes
[23:56:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:56:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:56:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:56:35] Found vcfuniq - /usr/local/bin/vcfuniq
[23:56:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:56:35] Found gzip - /bin/gzip
[23:56:35] Found vt - /usr/local/bin/vt
[23:56:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:56:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:56:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:56:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:56:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:56:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:56:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:56:36] Using reference: /jetstream2/scratch/main/jobs/72174392/inputs/dataset_c3278295-0534-4341-a983-519e27d93d98.dat
[23:56:36] Treating reference as 'fasta' format.
[23:56:36] Will use 1 CPU cores.
[23:56:36] Using read file: /jetstream2/scratch/main/jobs/72174392/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat
[23:56:36] Creating folder: Select_on_dataset_11
[23:56:36] Changing working directory: Select_on_dataset_11
[23:56:36] Creating reference folder: reference
[23:56:36] Extracting FASTA and GFF from reference.
[23:56:37] Wrote 1 sequences to ref.fa
[23:56:37] Wrote 0 features to ref.gff
[23:56:37] Freebayes will process 1 chunks of 12416664 bp, 1 chunks at a time.
[23:56:37] Using BAM RG (Read Group) ID: Select_on_dataset_11
[23:56:37] Running: samtools faidx reference/ref.fa 2>> snps.log
[23:56:37] Running: bwa index reference/ref.fa 2>> snps.log
[23:56:43] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[23:56:43] Running: ln -sf reference/ref.fa . 2>> snps.log
[23:56:43] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[23:56:43] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[23:56:43] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_11\tSM:Select_on_dataset_11' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72174392/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72174392/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72174392/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72174392/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences in reference/ref.fa.fai
[M::process] read 1 sequences (11639536 bp)...
[samclip] Total SAM records 0 |
| 1 | [04:37:18] This is snippy 4.6.0Show full stderr[04:37:18] This is snippy 4.6.0
[04:37:18] Written by Torsten Seemann
[04:37:18] Obtained from https://github.com/tseemann/snippy
[04:37:18] Detected operating system: linux
[04:37:18] Enabling bundled linux tools.
[04:37:18] Found bwa - /usr/local/bin/bwa
[04:37:18] Found bcftools - /usr/local/bin/bcftools
[04:37:18] Found samtools - /usr/local/bin/samtools
[04:37:18] Found java - /usr/local/bin/java
[04:37:18] Found snpEff - /usr/local/bin/snpEff
[04:37:18] Found samclip - /usr/local/bin/samclip
[04:37:18] Found seqtk - /usr/local/bin/seqtk
[04:37:18] Found parallel - /usr/local/bin/parallel
[04:37:18] Found freebayes - /usr/local/bin/freebayes
[04:37:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:18] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:18] Found gzip - /bin/gzip
[04:37:18] Found vt - /usr/local/bin/vt
[04:37:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:37:45] This is snippy 4.6.0Show full stderr[04:37:45] This is snippy 4.6.0
[04:37:45] Written by Torsten Seemann
[04:37:45] Obtained from https://github.com/tseemann/snippy
[04:37:45] Detected operating system: linux
[04:37:45] Enabling bundled linux tools.
[04:37:45] Found bwa - /usr/local/bin/bwa
[04:37:45] Found bcftools - /usr/local/bin/bcftools
[04:37:45] Found samtools - /usr/local/bin/samtools
[04:37:45] Found java - /usr/local/bin/java
[04:37:45] Found snpEff - /usr/local/bin/snpEff
[04:37:45] Found samclip - /usr/local/bin/samclip
[04:37:45] Found seqtk - /usr/local/bin/seqtk
[04:37:45] Found parallel - /usr/local/bin/parallel
[04:37:45] Found freebayes - /usr/local/bin/freebayes
[04:37:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:45] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:45] Found gzip - /bin/gzip
[04:37:45] Found vt - /usr/local/bin/vt
[04:37:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:38:27] This is snippy 4.6.0Show full stderr[04:38:27] This is snippy 4.6.0
[04:38:27] Written by Torsten Seemann
[04:38:27] Obtained from https://github.com/tseemann/snippy
[04:38:27] Detected operating system: linux
[04:38:27] Enabling bundled linux tools.
[04:38:27] Found bwa - /usr/local/bin/bwa
[04:38:27] Found bcftools - /usr/local/bin/bcftools
[04:38:27] Found samtools - /usr/local/bin/samtools
[04:38:27] Found java - /usr/local/bin/java
[04:38:27] Found snpEff - /usr/local/bin/snpEff
[04:38:27] Found samclip - /usr/local/bin/samclip
[04:38:27] Found seqtk - /usr/local/bin/seqtk
[04:38:27] Found parallel - /usr/local/bin/parallel
[04:38:27] Found freebayes - /usr/local/bin/freebayes
[04:38:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:27] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:27] Found gzip - /bin/gzip
[04:38:27] Found vt - /usr/local/bin/vt
[04:38:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:38:39] This is snippy 4.6.0Show full stderr[04:38:39] This is snippy 4.6.0
[04:38:39] Written by Torsten Seemann
[04:38:39] Obtained from https://github.com/tseemann/snippy
[04:38:39] Detected operating system: linux
[04:38:39] Enabling bundled linux tools.
[04:38:39] Found bwa - /usr/local/bin/bwa
[04:38:39] Found bcftools - /usr/local/bin/bcftools
[04:38:39] Found samtools - /usr/local/bin/samtools
[04:38:39] Found java - /usr/local/bin/java
[04:38:39] Found snpEff - /usr/local/bin/snpEff
[04:38:39] Found samclip - /usr/local/bin/samclip
[04:38:39] Found seqtk - /usr/local/bin/seqtk
[04:38:39] Found parallel - /usr/local/bin/parallel
[04:38:39] Found freebayes - /usr/local/bin/freebayes
[04:38:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:39] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:39] Found gzip - /bin/gzip
[04:38:39] Found vt - /usr/local/bin/vt
[04:38:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:36:57] This is snippy 4.6.0Show full stderr[04:36:57] This is snippy 4.6.0
[04:36:57] Written by Torsten Seemann
[04:36:57] Obtained from https://github.com/tseemann/snippy
[04:36:57] Detected operating system: linux
[04:36:57] Enabling bundled linux tools.
[04:36:57] Found bwa - /usr/local/bin/bwa
[04:36:57] Found bcftools - /usr/local/bin/bcftools
[04:36:57] Found samtools - /usr/local/bin/samtools
[04:36:57] Found java - /usr/local/bin/java
[04:36:57] Found snpEff - /usr/local/bin/snpEff
[04:36:57] Found samclip - /usr/local/bin/samclip
[04:36:57] Found seqtk - /usr/local/bin/seqtk
[04:36:57] Found parallel - /usr/local/bin/parallel
[04:36:57] Found freebayes - /usr/local/bin/freebayes
[04:36:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:36:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:36:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:36:57] Found vcfuniq - /usr/local/bin/vcfuniq
[04:36:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:36:57] Found gzip - /bin/gzip
[04:36:57] Found vt - /usr/local/bin/vt
[04:36:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:36:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:36:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:36:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:36:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:36:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:36:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:36:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:38:48] This is snippy 4.6.0Show full stderr[04:38:48] This is snippy 4.6.0
[04:38:48] Written by Torsten Seemann
[04:38:48] Obtained from https://github.com/tseemann/snippy
[04:38:48] Detected operating system: linux
[04:38:48] Enabling bundled linux tools.
[04:38:48] Found bwa - /usr/local/bin/bwa
[04:38:48] Found bcftools - /usr/local/bin/bcftools
[04:38:48] Found samtools - /usr/local/bin/samtools
[04:38:48] Found java - /usr/local/bin/java
[04:38:48] Found snpEff - /usr/local/bin/snpEff
[04:38:48] Found samclip - /usr/local/bin/samclip
[04:38:48] Found seqtk - /usr/local/bin/seqtk
[04:38:48] Found parallel - /usr/local/bin/parallel
[04:38:48] Found freebayes - /usr/local/bin/freebayes
[04:38:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:48] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:48] Found gzip - /bin/gzip
[04:38:48] Found vt - /usr/local/bin/vt
[04:38:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:39:54] This is snippy 4.6.0Show full stderr[04:39:54] This is snippy 4.6.0
[04:39:54] Written by Torsten Seemann
[04:39:54] Obtained from https://github.com/tseemann/snippy
[04:39:54] Detected operating system: linux
[04:39:54] Enabling bundled linux tools.
[04:39:54] Found bwa - /usr/local/bin/bwa
[04:39:54] Found bcftools - /usr/local/bin/bcftools
[04:39:54] Found samtools - /usr/local/bin/samtools
[04:39:54] Found java - /usr/local/bin/java
[04:39:54] Found snpEff - /usr/local/bin/snpEff
[04:39:54] Found samclip - /usr/local/bin/samclip
[04:39:54] Found seqtk - /usr/local/bin/seqtk
[04:39:54] Found parallel - /usr/local/bin/parallel
[04:39:54] Found freebayes - /usr/local/bin/freebayes
[04:39:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:39:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:39:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:39:54] Found vcfuniq - /usr/local/bin/vcfuniq
[04:39:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:39:54] Found gzip - /bin/gzip
[04:39:54] Found vt - /usr/local/bin/vt
[04:39:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:39:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:39:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:39:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:39:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:39:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:39:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:39:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:37:12] This is snippy 4.6.0Show full stderr[04:37:12] This is snippy 4.6.0
[04:37:12] Written by Torsten Seemann
[04:37:12] Obtained from https://github.com/tseemann/snippy
[04:37:12] Detected operating system: linux
[04:37:12] Enabling bundled linux tools.
[04:37:12] Found bwa - /usr/local/bin/bwa
[04:37:12] Found bcftools - /usr/local/bin/bcftools
[04:37:12] Found samtools - /usr/local/bin/samtools
[04:37:12] Found java - /usr/local/bin/java
[04:37:12] Found snpEff - /usr/local/bin/snpEff
[04:37:12] Found samclip - /usr/local/bin/samclip
[04:37:12] Found seqtk - /usr/local/bin/seqtk
[04:37:12] Found parallel - /usr/local/bin/parallel
[04:37:12] Found freebayes - /usr/local/bin/freebayes
[04:37:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:12] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:12] Found gzip - /bin/gzip
[04:37:12] Found vt - /usr/local/bin/vt
[04:37:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:37:30] This is snippy 4.6.0Show full stderr[04:37:30] This is snippy 4.6.0
[04:37:30] Written by Torsten Seemann
[04:37:30] Obtained from https://github.com/tseemann/snippy
[04:37:30] Detected operating system: linux
[04:37:30] Enabling bundled linux tools.
[04:37:30] Found bwa - /usr/local/bin/bwa
[04:37:30] Found bcftools - /usr/local/bin/bcftools
[04:37:30] Found samtools - /usr/local/bin/samtools
[04:37:30] Found java - /usr/local/bin/java
[04:37:30] Found snpEff - /usr/local/bin/snpEff
[04:37:30] Found samclip - /usr/local/bin/samclip
[04:37:30] Found seqtk - /usr/local/bin/seqtk
[04:37:30] Found parallel - /usr/local/bin/parallel
[04:37:30] Found freebayes - /usr/local/bin/freebayes
[04:37:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:30] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:30] Found gzip - /bin/gzip
[04:37:30] Found vt - /usr/local/bin/vt
[04:37:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:38:33] This is snippy 4.6.0Show full stderr[04:38:33] This is snippy 4.6.0
[04:38:33] Written by Torsten Seemann
[04:38:33] Obtained from https://github.com/tseemann/snippy
[04:38:33] Detected operating system: linux
[04:38:33] Enabling bundled linux tools.
[04:38:33] Found bwa - /usr/local/bin/bwa
[04:38:33] Found bcftools - /usr/local/bin/bcftools
[04:38:33] Found samtools - /usr/local/bin/samtools
[04:38:33] Found java - /usr/local/bin/java
[04:38:33] Found snpEff - /usr/local/bin/snpEff
[04:38:33] Found samclip - /usr/local/bin/samclip
[04:38:33] Found seqtk - /usr/local/bin/seqtk
[04:38:33] Found parallel - /usr/local/bin/parallel
[04:38:33] Found freebayes - /usr/local/bin/freebayes
[04:38:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:33] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:33] Found gzip - /bin/gzip
[04:38:33] Found vt - /usr/local/bin/vt
[04:38:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:37:21] This is snippy 4.6.0Show full stderr[04:37:21] This is snippy 4.6.0
[04:37:21] Written by Torsten Seemann
[04:37:21] Obtained from https://github.com/tseemann/snippy
[04:37:21] Detected operating system: linux
[04:37:21] Enabling bundled linux tools.
[04:37:21] Found bwa - /usr/local/bin/bwa
[04:37:21] Found bcftools - /usr/local/bin/bcftools
[04:37:21] Found samtools - /usr/local/bin/samtools
[04:37:21] Found java - /usr/local/bin/java
[04:37:21] Found snpEff - /usr/local/bin/snpEff
[04:37:21] Found samclip - /usr/local/bin/samclip
[04:37:21] Found seqtk - /usr/local/bin/seqtk
[04:37:21] Found parallel - /usr/local/bin/parallel
[04:37:21] Found freebayes - /usr/local/bin/freebayes
[04:37:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:21] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:21] Found gzip - /bin/gzip
[04:37:21] Found vt - /usr/local/bin/vt
[04:37:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:37:36] This is snippy 4.6.0Show full stderr[04:37:36] This is snippy 4.6.0
[04:37:36] Written by Torsten Seemann
[04:37:36] Obtained from https://github.com/tseemann/snippy
[04:37:36] Detected operating system: linux
[04:37:36] Enabling bundled linux tools.
[04:37:36] Found bwa - /usr/local/bin/bwa
[04:37:36] Found bcftools - /usr/local/bin/bcftools
[04:37:36] Found samtools - /usr/local/bin/samtools
[04:37:36] Found java - /usr/local/bin/java
[04:37:36] Found snpEff - /usr/local/bin/snpEff
[04:37:36] Found samclip - /usr/local/bin/samclip
[04:37:36] Found seqtk - /usr/local/bin/seqtk
[04:37:36] Found parallel - /usr/local/bin/parallel
[04:37:36] Found freebayes - /usr/local/bin/freebayes
[04:37:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:37:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:37:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:37:36] Found vcfuniq - /usr/local/bin/vcfuniq
[04:37:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:37:36] Found gzip - /bin/gzip
[04:37:36] Found vt - /usr/local/bin/vt
[04:37:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:37:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:37:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:37:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:37:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:37:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:37:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:37:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:38:42] This is snippy 4.6.0Show full stderr[04:38:42] This is snippy 4.6.0
[04:38:42] Written by Torsten Seemann
[04:38:42] Obtained from https://github.com/tseemann/snippy
[04:38:42] Detected operating system: linux
[04:38:42] Enabling bundled linux tools.
[04:38:42] Found bwa - /usr/local/bin/bwa
[04:38:42] Found bcftools - /usr/local/bin/bcftools
[04:38:42] Found samtools - /usr/local/bin/samtools
[04:38:42] Found java - /usr/local/bin/java
[04:38:42] Found snpEff - /usr/local/bin/snpEff
[04:38:42] Found samclip - /usr/local/bin/samclip
[04:38:42] Found seqtk - /usr/local/bin/seqtk
[04:38:42] Found parallel - /usr/local/bin/parallel
[04:38:42] Found freebayes - /usr/local/bin/freebayes
[04:38:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:42] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:42] Found gzip - /bin/gzip
[04:38:42] Found vt - /usr/local/bin/vt
[04:38:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:38:45] This is snippy 4.6.0Show full stderr[04:38:45] This is snippy 4.6.0
[04:38:45] Written by Torsten Seemann
[04:38:45] Obtained from https://github.com/tseemann/snippy
[04:38:45] Detected operating system: linux
[04:38:45] Enabling bundled linux tools.
[04:38:45] Found bwa - /usr/local/bin/bwa
[04:38:45] Found bcftools - /usr/local/bin/bcftools
[04:38:45] Found samtools - /usr/local/bin/samtools
[04:38:45] Found java - /usr/local/bin/java
[04:38:45] Found snpEff - /usr/local/bin/snpEff
[04:38:45] Found samclip - /usr/local/bin/samclip
[04:38:45] Found seqtk - /usr/local/bin/seqtk
[04:38:45] Found parallel - /usr/local/bin/parallel
[04:38:45] Found freebayes - /usr/local/bin/freebayes
[04:38:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:45] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:45] Found gzip - /bin/gzip
[04:38:45] Found vt - /usr/local/bin/vt
[04:38:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:38:57] This is snippy 4.6.0Show full stderr[04:38:57] This is snippy 4.6.0
[04:38:57] Written by Torsten Seemann
[04:38:57] Obtained from https://github.com/tseemann/snippy
[04:38:57] Detected operating system: linux
[04:38:57] Enabling bundled linux tools.
[04:38:57] Found bwa - /usr/local/bin/bwa
[04:38:57] Found bcftools - /usr/local/bin/bcftools
[04:38:57] Found samtools - /usr/local/bin/samtools
[04:38:57] Found java - /usr/local/bin/java
[04:38:57] Found snpEff - /usr/local/bin/snpEff
[04:38:57] Found samclip - /usr/local/bin/samclip
[04:38:57] Found seqtk - /usr/local/bin/seqtk
[04:38:57] Found parallel - /usr/local/bin/parallel
[04:38:57] Found freebayes - /usr/local/bin/freebayes
[04:38:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:38:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:38:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:38:57] Found vcfuniq - /usr/local/bin/vcfuniq
[04:38:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:38:57] Found gzip - /bin/gzip
[04:38:57] Found vt - /usr/local/bin/vt
[04:38:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:38:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:38:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:38:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:38:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:38:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:38:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:38:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:39:42] This is snippy 4.6.0Show full stderr[04:39:42] This is snippy 4.6.0
[04:39:42] Written by Torsten Seemann
[04:39:42] Obtained from https://github.com/tseemann/snippy
[04:39:42] Detected operating system: linux
[04:39:42] Enabling bundled linux tools.
[04:39:42] Found bwa - /usr/local/bin/bwa
[04:39:42] Found bcftools - /usr/local/bin/bcftools
[04:39:42] Found samtools - /usr/local/bin/samtools
[04:39:42] Found java - /usr/local/bin/java
[04:39:42] Found snpEff - /usr/local/bin/snpEff
[04:39:42] Found samclip - /usr/local/bin/samclip
[04:39:42] Found seqtk - /usr/local/bin/seqtk
[04:39:42] Found parallel - /usr/local/bin/parallel
[04:39:42] Found freebayes - /usr/local/bin/freebayes
[04:39:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:39:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:39:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:39:42] Found vcfuniq - /usr/local/bin/vcfuniq
[04:39:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:39:42] Found gzip - /bin/gzip
[04:39:42] Found vt - /usr/local/bin/vt
[04:39:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:39:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:39:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:39:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:39:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:39:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:39:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:39:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:40:42] This is snippy 4.6.0Show full stderr[04:40:42] This is snippy 4.6.0
[04:40:42] Written by Torsten Seemann
[04:40:42] Obtained from https://github.com/tseemann/snippy
[04:40:42] Detected operating system: linux
[04:40:42] Enabling bundled linux tools.
[04:40:42] Found bwa - /usr/local/bin/bwa
[04:40:42] Found bcftools - /usr/local/bin/bcftools
[04:40:42] Found samtools - /usr/local/bin/samtools
[04:40:42] Found java - /usr/local/bin/java
[04:40:42] Found snpEff - /usr/local/bin/snpEff
[04:40:42] Found samclip - /usr/local/bin/samclip
[04:40:42] Found seqtk - /usr/local/bin/seqtk
[04:40:42] Found parallel - /usr/local/bin/parallel
[04:40:42] Found freebayes - /usr/local/bin/freebayes
[04:40:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:42] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:42] Found gzip - /bin/gzip
[04:40:42] Found vt - /usr/local/bin/vt
[04:40:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:40:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:40:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:40:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:41:15] This is snippy 4.6.0Show full stderr[04:41:15] This is snippy 4.6.0
[04:41:15] Written by Torsten Seemann
[04:41:15] Obtained from https://github.com/tseemann/snippy
[04:41:15] Detected operating system: linux
[04:41:15] Enabling bundled linux tools.
[04:41:15] Found bwa - /usr/local/bin/bwa
[04:41:15] Found bcftools - /usr/local/bin/bcftools
[04:41:15] Found samtools - /usr/local/bin/samtools
[04:41:15] Found java - /usr/local/bin/java
[04:41:15] Found snpEff - /usr/local/bin/snpEff
[04:41:15] Found samclip - /usr/local/bin/samclip
[04:41:15] Found seqtk - /usr/local/bin/seqtk
[04:41:15] Found parallel - /usr/local/bin/parallel
[04:41:15] Found freebayes - /usr/local/bin/freebayes
[04:41:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:15] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:15] Found gzip - /bin/gzip
[04:41:15] Found vt - /usr/local/bin/vt
[04:41:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:41:40] This is snippy 4.6.0Show full stderr[04:41:40] This is snippy 4.6.0
[04:41:40] Written by Torsten Seemann
[04:41:40] Obtained from https://github.com/tseemann/snippy
[04:41:40] Detected operating system: linux
[04:41:40] Enabling bundled linux tools.
[04:41:40] Found bwa - /usr/local/bin/bwa
[04:41:40] Found bcftools - /usr/local/bin/bcftools
[04:41:40] Found samtools - /usr/local/bin/samtools
[04:41:40] Found java - /usr/local/bin/java
[04:41:40] Found snpEff - /usr/local/bin/snpEff
[04:41:40] Found samclip - /usr/local/bin/samclip
[04:41:40] Found seqtk - /usr/local/bin/seqtk
[04:41:40] Found parallel - /usr/local/bin/parallel
[04:41:40] Found freebayes - /usr/local/bin/freebayes
[04:41:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:40] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:40] Found gzip - /bin/gzip
[04:41:40] Found vt - /usr/local/bin/vt
[04:41:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:42:07] This is snippy 4.6.0Show full stderr[04:42:07] This is snippy 4.6.0
[04:42:07] Written by Torsten Seemann
[04:42:07] Obtained from https://github.com/tseemann/snippy
[04:42:07] Detected operating system: linux
[04:42:07] Enabling bundled linux tools.
[04:42:07] Found bwa - /usr/local/bin/bwa
[04:42:07] Found bcftools - /usr/local/bin/bcftools
[04:42:07] Found samtools - /usr/local/bin/samtools
[04:42:07] Found java - /usr/local/bin/java
[04:42:07] Found snpEff - /usr/local/bin/snpEff
[04:42:07] Found samclip - /usr/local/bin/samclip
[04:42:07] Found seqtk - /usr/local/bin/seqtk
[04:42:07] Found parallel - /usr/local/bin/parallel
[04:42:07] Found freebayes - /usr/local/bin/freebayes
[04:42:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:07] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:07] Found gzip - /bin/gzip
[04:42:07] Found vt - /usr/local/bin/vt
[04:42:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:42:17] This is snippy 4.6.0Show full stderr[04:42:17] This is snippy 4.6.0
[04:42:17] Written by Torsten Seemann
[04:42:17] Obtained from https://github.com/tseemann/snippy
[04:42:17] Detected operating system: linux
[04:42:17] Enabling bundled linux tools.
[04:42:17] Found bwa - /usr/local/bin/bwa
[04:42:17] Found bcftools - /usr/local/bin/bcftools
[04:42:17] Found samtools - /usr/local/bin/samtools
[04:42:17] Found java - /usr/local/bin/java
[04:42:17] Found snpEff - /usr/local/bin/snpEff
[04:42:17] Found samclip - /usr/local/bin/samclip
[04:42:17] Found seqtk - /usr/local/bin/seqtk
[04:42:17] Found parallel - /usr/local/bin/parallel
[04:42:17] Found freebayes - /usr/local/bin/freebayes
[04:42:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:17] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:17] Found gzip - /bin/gzip
[04:42:17] Found vt - /usr/local/bin/vt
[04:42:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:42:12] This is snippy 4.6.0Show full stderr[04:42:12] This is snippy 4.6.0
[04:42:12] Written by Torsten Seemann
[04:42:12] Obtained from https://github.com/tseemann/snippy
[04:42:12] Detected operating system: linux
[04:42:12] Enabling bundled linux tools.
[04:42:12] Found bwa - /usr/local/bin/bwa
[04:42:12] Found bcftools - /usr/local/bin/bcftools
[04:42:12] Found samtools - /usr/local/bin/samtools
[04:42:12] Found java - /usr/local/bin/java
[04:42:12] Found snpEff - /usr/local/bin/snpEff
[04:42:12] Found samclip - /usr/local/bin/samclip
[04:42:12] Found seqtk - /usr/local/bin/seqtk
[04:42:12] Found parallel - /usr/local/bin/parallel
[04:42:12] Found freebayes - /usr/local/bin/freebayes
[04:42:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:12] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:12] Found gzip - /bin/gzip
[04:42:12] Found vt - /usr/local/bin/vt
[04:42:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:42:13] This is snippy 4.6.0Show full stderr[04:42:13] This is snippy 4.6.0
[04:42:13] Written by Torsten Seemann
[04:42:13] Obtained from https://github.com/tseemann/snippy
[04:42:13] Detected operating system: linux
[04:42:13] Enabling bundled linux tools.
[04:42:13] Found bwa - /usr/local/bin/bwa
[04:42:13] Found bcftools - /usr/local/bin/bcftools
[04:42:13] Found samtools - /usr/local/bin/samtools
[04:42:13] Found java - /usr/local/bin/java
[04:42:13] Found snpEff - /usr/local/bin/snpEff
[04:42:13] Found samclip - /usr/local/bin/samclip
[04:42:13] Found seqtk - /usr/local/bin/seqtk
[04:42:13] Found parallel - /usr/local/bin/parallel
[04:42:13] Found freebayes - /usr/local/bin/freebayes
[04:42:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:13] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:13] Found gzip - /bin/gzip
[04:42:13] Found vt - /usr/local/bin/vt
[04:42:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:40:35] This is snippy 4.6.0Show full stderr[04:40:35] This is snippy 4.6.0
[04:40:35] Written by Torsten Seemann
[04:40:35] Obtained from https://github.com/tseemann/snippy
[04:40:35] Detected operating system: linux
[04:40:35] Enabling bundled linux tools.
[04:40:35] Found bwa - /usr/local/bin/bwa
[04:40:35] Found bcftools - /usr/local/bin/bcftools
[04:40:35] Found samtools - /usr/local/bin/samtools
[04:40:35] Found java - /usr/local/bin/java
[04:40:35] Found snpEff - /usr/local/bin/snpEff
[04:40:35] Found samclip - /usr/local/bin/samclip
[04:40:35] Found seqtk - /usr/local/bin/seqtk
[04:40:35] Found parallel - /usr/local/bin/parallel
[04:40:35] Found freebayes - /usr/local/bin/freebayes
[04:40:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:35] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:35] Found gzip - /bin/gzip
[04:40:35] Found vt - /usr/local/bin/vt
[04:40:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:40:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:40:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:40:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:41:03] This is snippy 4.6.0Show full stderr[04:41:03] This is snippy 4.6.0
[04:41:03] Written by Torsten Seemann
[04:41:03] Obtained from https://github.com/tseemann/snippy
[04:41:03] Detected operating system: linux
[04:41:03] Enabling bundled linux tools.
[04:41:03] Found bwa - /usr/local/bin/bwa
[04:41:03] Found bcftools - /usr/local/bin/bcftools
[04:41:03] Found samtools - /usr/local/bin/samtools
[04:41:03] Found java - /usr/local/bin/java
[04:41:03] Found snpEff - /usr/local/bin/snpEff
[04:41:03] Found samclip - /usr/local/bin/samclip
[04:41:03] Found seqtk - /usr/local/bin/seqtk
[04:41:03] Found parallel - /usr/local/bin/parallel
[04:41:03] Found freebayes - /usr/local/bin/freebayes
[04:41:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:03] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:03] Found gzip - /bin/gzip
[04:41:03] Found vt - /usr/local/bin/vt
[04:41:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:41:52] This is snippy 4.6.0Show full stderr[04:41:52] This is snippy 4.6.0
[04:41:52] Written by Torsten Seemann
[04:41:52] Obtained from https://github.com/tseemann/snippy
[04:41:52] Detected operating system: linux
[04:41:52] Enabling bundled linux tools.
[04:41:52] Found bwa - /usr/local/bin/bwa
[04:41:52] Found bcftools - /usr/local/bin/bcftools
[04:41:52] Found samtools - /usr/local/bin/samtools
[04:41:52] Found java - /usr/local/bin/java
[04:41:52] Found snpEff - /usr/local/bin/snpEff
[04:41:52] Found samclip - /usr/local/bin/samclip
[04:41:52] Found seqtk - /usr/local/bin/seqtk
[04:41:52] Found parallel - /usr/local/bin/parallel
[04:41:52] Found freebayes - /usr/local/bin/freebayes
[04:41:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:52] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:52] Found gzip - /bin/gzip
[04:41:52] Found vt - /usr/local/bin/vt
[04:41:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:42:36] This is snippy 4.6.0Show full stderr[04:42:36] This is snippy 4.6.0
[04:42:36] Written by Torsten Seemann
[04:42:36] Obtained from https://github.com/tseemann/snippy
[04:42:36] Detected operating system: linux
[04:42:36] Enabling bundled linux tools.
[04:42:36] Found bwa - /usr/local/bin/bwa
[04:42:36] Found bcftools - /usr/local/bin/bcftools
[04:42:36] Found samtools - /usr/local/bin/samtools
[04:42:36] Found java - /usr/local/bin/java
[04:42:36] Found snpEff - /usr/local/bin/snpEff
[04:42:36] Found samclip - /usr/local/bin/samclip
[04:42:36] Found seqtk - /usr/local/bin/seqtk
[04:42:36] Found parallel - /usr/local/bin/parallel
[04:42:36] Found freebayes - /usr/local/bin/freebayes
[04:42:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:36] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:36] Found gzip - /bin/gzip
[04:42:36] Found vt - /usr/local/bin/vt
[04:42:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:42:44] This is snippy 4.6.0Show full stderr[04:42:44] This is snippy 4.6.0
[04:42:44] Written by Torsten Seemann
[04:42:44] Obtained from https://github.com/tseemann/snippy
[04:42:44] Detected operating system: linux
[04:42:44] Enabling bundled linux tools.
[04:42:44] Found bwa - /usr/local/bin/bwa
[04:42:44] Found bcftools - /usr/local/bin/bcftools
[04:42:44] Found samtools - /usr/local/bin/samtools
[04:42:44] Found java - /usr/local/bin/java
[04:42:44] Found snpEff - /usr/local/bin/snpEff
[04:42:44] Found samclip - /usr/local/bin/samclip
[04:42:44] Found seqtk - /usr/local/bin/seqtk
[04:42:44] Found parallel - /usr/local/bin/parallel
[04:42:44] Found freebayes - /usr/local/bin/freebayes
[04:42:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:44] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:44] Found gzip - /bin/gzip
[04:42:44] Found vt - /usr/local/bin/vt
[04:42:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:40:59] This is snippy 4.6.0Show full stderr[04:40:59] This is snippy 4.6.0
[04:40:59] Written by Torsten Seemann
[04:40:59] Obtained from https://github.com/tseemann/snippy
[04:40:59] Detected operating system: linux
[04:40:59] Enabling bundled linux tools.
[04:40:59] Found bwa - /usr/local/bin/bwa
[04:40:59] Found bcftools - /usr/local/bin/bcftools
[04:40:59] Found samtools - /usr/local/bin/samtools
[04:40:59] Found java - /usr/local/bin/java
[04:40:59] Found snpEff - /usr/local/bin/snpEff
[04:40:59] Found samclip - /usr/local/bin/samclip
[04:40:59] Found seqtk - /usr/local/bin/seqtk
[04:40:59] Found parallel - /usr/local/bin/parallel
[04:40:59] Found freebayes - /usr/local/bin/freebayes
[04:40:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:40:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:40:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:40:59] Found vcfuniq - /usr/local/bin/vcfuniq
[04:40:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:40:59] Found gzip - /bin/gzip
[04:40:59] Found vt - /usr/local/bin/vt
[04:40:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:40:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:40:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:40:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:40:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:41:06] This is snippy 4.6.0Show full stderr[04:41:06] This is snippy 4.6.0
[04:41:06] Written by Torsten Seemann
[04:41:06] Obtained from https://github.com/tseemann/snippy
[04:41:06] Detected operating system: linux
[04:41:06] Enabling bundled linux tools.
[04:41:06] Found bwa - /usr/local/bin/bwa
[04:41:06] Found bcftools - /usr/local/bin/bcftools
[04:41:06] Found samtools - /usr/local/bin/samtools
[04:41:06] Found java - /usr/local/bin/java
[04:41:06] Found snpEff - /usr/local/bin/snpEff
[04:41:06] Found samclip - /usr/local/bin/samclip
[04:41:06] Found seqtk - /usr/local/bin/seqtk
[04:41:06] Found parallel - /usr/local/bin/parallel
[04:41:06] Found freebayes - /usr/local/bin/freebayes
[04:41:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:06] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:06] Found gzip - /bin/gzip
[04:41:06] Found vt - /usr/local/bin/vt
[04:41:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:41:12] This is snippy 4.6.0Show full stderr[04:41:12] This is snippy 4.6.0
[04:41:12] Written by Torsten Seemann
[04:41:12] Obtained from https://github.com/tseemann/snippy
[04:41:12] Detected operating system: linux
[04:41:12] Enabling bundled linux tools.
[04:41:12] Found bwa - /usr/local/bin/bwa
[04:41:12] Found bcftools - /usr/local/bin/bcftools
[04:41:12] Found samtools - /usr/local/bin/samtools
[04:41:12] Found java - /usr/local/bin/java
[04:41:12] Found snpEff - /usr/local/bin/snpEff
[04:41:12] Found samclip - /usr/local/bin/samclip
[04:41:12] Found seqtk - /usr/local/bin/seqtk
[04:41:12] Found parallel - /usr/local/bin/parallel
[04:41:12] Found freebayes - /usr/local/bin/freebayes
[04:41:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:12] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:12] Found gzip - /bin/gzip
[04:41:12] Found vt - /usr/local/bin/vt
[04:41:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:41:27] This is snippy 4.6.0Show full stderr[04:41:27] This is snippy 4.6.0
[04:41:27] Written by Torsten Seemann
[04:41:27] Obtained from https://github.com/tseemann/snippy
[04:41:27] Detected operating system: linux
[04:41:27] Enabling bundled linux tools.
[04:41:27] Found bwa - /usr/local/bin/bwa
[04:41:27] Found bcftools - /usr/local/bin/bcftools
[04:41:27] Found samtools - /usr/local/bin/samtools
[04:41:27] Found java - /usr/local/bin/java
[04:41:27] Found snpEff - /usr/local/bin/snpEff
[04:41:27] Found samclip - /usr/local/bin/samclip
[04:41:27] Found seqtk - /usr/local/bin/seqtk
[04:41:27] Found parallel - /usr/local/bin/parallel
[04:41:27] Found freebayes - /usr/local/bin/freebayes
[04:41:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:41:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:41:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:41:27] Found vcfuniq - /usr/local/bin/vcfuniq
[04:41:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:41:27] Found gzip - /bin/gzip
[04:41:27] Found vt - /usr/local/bin/vt
[04:41:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:41:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:41:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:41:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:41:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:41:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:41:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:41:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:42:39] This is snippy 4.6.0Show full stderr[04:42:39] This is snippy 4.6.0
[04:42:39] Written by Torsten Seemann
[04:42:39] Obtained from https://github.com/tseemann/snippy
[04:42:39] Detected operating system: linux
[04:42:39] Enabling bundled linux tools.
[04:42:39] Found bwa - /usr/local/bin/bwa
[04:42:39] Found bcftools - /usr/local/bin/bcftools
[04:42:39] Found samtools - /usr/local/bin/samtools
[04:42:39] Found java - /usr/local/bin/java
[04:42:40] Found snpEff - /usr/local/bin/snpEff
[04:42:40] Found samclip - /usr/local/bin/samclip
[04:42:40] Found seqtk - /usr/local/bin/seqtk
[04:42:40] Found parallel - /usr/local/bin/parallel
[04:42:40] Found freebayes - /usr/local/bin/freebayes
[04:42:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:40] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:40] Found gzip - /bin/gzip
[04:42:40] Found vt - /usr/local/bin/vt
[04:42:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:00] This is snippy 4.6.0Show full stderr[04:43:00] This is snippy 4.6.0
[04:43:00] Written by Torsten Seemann
[04:43:00] Obtained from https://github.com/tseemann/snippy
[04:43:00] Detected operating system: linux
[04:43:00] Enabling bundled linux tools.
[04:43:00] Found bwa - /usr/local/bin/bwa
[04:43:00] Found bcftools - /usr/local/bin/bcftools
[04:43:00] Found samtools - /usr/local/bin/samtools
[04:43:00] Found java - /usr/local/bin/java
[04:43:00] Found snpEff - /usr/local/bin/snpEff
[04:43:00] Found samclip - /usr/local/bin/samclip
[04:43:00] Found seqtk - /usr/local/bin/seqtk
[04:43:00] Found parallel - /usr/local/bin/parallel
[04:43:00] Found freebayes - /usr/local/bin/freebayes
[04:43:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:00] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:00] Found gzip - /bin/gzip
[04:43:00] Found vt - /usr/local/bin/vt
[04:43:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:34] This is snippy 4.6.0Show full stderr[04:43:34] This is snippy 4.6.0
[04:43:34] Written by Torsten Seemann
[04:43:34] Obtained from https://github.com/tseemann/snippy
[04:43:34] Detected operating system: linux
[04:43:34] Enabling bundled linux tools.
[04:43:34] Found bwa - /usr/local/bin/bwa
[04:43:34] Found bcftools - /usr/local/bin/bcftools
[04:43:34] Found samtools - /usr/local/bin/samtools
[04:43:34] Found java - /usr/local/bin/java
[04:43:34] Found snpEff - /usr/local/bin/snpEff
[04:43:34] Found samclip - /usr/local/bin/samclip
[04:43:34] Found seqtk - /usr/local/bin/seqtk
[04:43:34] Found parallel - /usr/local/bin/parallel
[04:43:34] Found freebayes - /usr/local/bin/freebayes
[04:43:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:34] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:34] Found gzip - /bin/gzip
[04:43:34] Found vt - /usr/local/bin/vt
[04:43:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:44:12] This is snippy 4.6.0Show full stderr[04:44:12] This is snippy 4.6.0
[04:44:12] Written by Torsten Seemann
[04:44:12] Obtained from https://github.com/tseemann/snippy
[04:44:12] Detected operating system: linux
[04:44:12] Enabling bundled linux tools.
[04:44:12] Found bwa - /usr/local/bin/bwa
[04:44:12] Found bcftools - /usr/local/bin/bcftools
[04:44:12] Found samtools - /usr/local/bin/samtools
[04:44:12] Found java - /usr/local/bin/java
[04:44:12] Found snpEff - /usr/local/bin/snpEff
[04:44:12] Found samclip - /usr/local/bin/samclip
[04:44:12] Found seqtk - /usr/local/bin/seqtk
[04:44:12] Found parallel - /usr/local/bin/parallel
[04:44:12] Found freebayes - /usr/local/bin/freebayes
[04:44:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:12] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:12] Found gzip - /bin/gzip
[04:44:12] Found vt - /usr/local/bin/vt
[04:44:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:44:16] This is snippy 4.6.0Show full stderr[04:44:16] This is snippy 4.6.0
[04:44:16] Written by Torsten Seemann
[04:44:16] Obtained from https://github.com/tseemann/snippy
[04:44:16] Detected operating system: linux
[04:44:16] Enabling bundled linux tools.
[04:44:16] Found bwa - /usr/local/bin/bwa
[04:44:16] Found bcftools - /usr/local/bin/bcftools
[04:44:16] Found samtools - /usr/local/bin/samtools
[04:44:16] Found java - /usr/local/bin/java
[04:44:16] Found snpEff - /usr/local/bin/snpEff
[04:44:16] Found samclip - /usr/local/bin/samclip
[04:44:16] Found seqtk - /usr/local/bin/seqtk
[04:44:16] Found parallel - /usr/local/bin/parallel
[04:44:16] Found freebayes - /usr/local/bin/freebayes
[04:44:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:16] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:16] Found gzip - /bin/gzip
[04:44:16] Found vt - /usr/local/bin/vt
[04:44:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:44:28] This is snippy 4.6.0Show full stderr[04:44:28] This is snippy 4.6.0
[04:44:28] Written by Torsten Seemann
[04:44:28] Obtained from https://github.com/tseemann/snippy
[04:44:28] Detected operating system: linux
[04:44:28] Enabling bundled linux tools.
[04:44:28] Found bwa - /usr/local/bin/bwa
[04:44:28] Found bcftools - /usr/local/bin/bcftools
[04:44:28] Found samtools - /usr/local/bin/samtools
[04:44:28] Found java - /usr/local/bin/java
[04:44:28] Found snpEff - /usr/local/bin/snpEff
[04:44:28] Found samclip - /usr/local/bin/samclip
[04:44:28] Found seqtk - /usr/local/bin/seqtk
[04:44:28] Found parallel - /usr/local/bin/parallel
[04:44:28] Found freebayes - /usr/local/bin/freebayes
[04:44:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:28] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:28] Found gzip - /bin/gzip
[04:44:28] Found vt - /usr/local/bin/vt
[04:44:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:44:49] This is snippy 4.6.0Show full stderr[04:44:49] This is snippy 4.6.0
[04:44:49] Written by Torsten Seemann
[04:44:49] Obtained from https://github.com/tseemann/snippy
[04:44:49] Detected operating system: linux
[04:44:49] Enabling bundled linux tools.
[04:44:49] Found bwa - /usr/local/bin/bwa
[04:44:49] Found bcftools - /usr/local/bin/bcftools
[04:44:49] Found samtools - /usr/local/bin/samtools
[04:44:49] Found java - /usr/local/bin/java
[04:44:49] Found snpEff - /usr/local/bin/snpEff
[04:44:49] Found samclip - /usr/local/bin/samclip
[04:44:49] Found seqtk - /usr/local/bin/seqtk
[04:44:49] Found parallel - /usr/local/bin/parallel
[04:44:49] Found freebayes - /usr/local/bin/freebayes
[04:44:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:49] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:49] Found gzip - /bin/gzip
[04:44:49] Found vt - /usr/local/bin/vt
[04:44:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:12] This is snippy 4.6.0Show full stderr[04:43:12] This is snippy 4.6.0
[04:43:12] Written by Torsten Seemann
[04:43:12] Obtained from https://github.com/tseemann/snippy
[04:43:12] Detected operating system: linux
[04:43:12] Enabling bundled linux tools.
[04:43:12] Found bwa - /usr/local/bin/bwa
[04:43:12] Found bcftools - /usr/local/bin/bcftools
[04:43:12] Found samtools - /usr/local/bin/samtools
[04:43:12] Found java - /usr/local/bin/java
[04:43:12] Found snpEff - /usr/local/bin/snpEff
[04:43:12] Found samclip - /usr/local/bin/samclip
[04:43:12] Found seqtk - /usr/local/bin/seqtk
[04:43:12] Found parallel - /usr/local/bin/parallel
[04:43:12] Found freebayes - /usr/local/bin/freebayes
[04:43:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:12] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:12] Found gzip - /bin/gzip
[04:43:12] Found vt - /usr/local/bin/vt
[04:43:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:18] This is snippy 4.6.0Show full stderr[04:43:18] This is snippy 4.6.0
[04:43:18] Written by Torsten Seemann
[04:43:18] Obtained from https://github.com/tseemann/snippy
[04:43:18] Detected operating system: linux
[04:43:18] Enabling bundled linux tools.
[04:43:18] Found bwa - /usr/local/bin/bwa
[04:43:18] Found bcftools - /usr/local/bin/bcftools
[04:43:18] Found samtools - /usr/local/bin/samtools
[04:43:18] Found java - /usr/local/bin/java
[04:43:18] Found snpEff - /usr/local/bin/snpEff
[04:43:18] Found samclip - /usr/local/bin/samclip
[04:43:18] Found seqtk - /usr/local/bin/seqtk
[04:43:18] Found parallel - /usr/local/bin/parallel
[04:43:18] Found freebayes - /usr/local/bin/freebayes
[04:43:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:18] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:18] Found gzip - /bin/gzip
[04:43:18] Found vt - /usr/local/bin/vt
[04:43:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:27] This is snippy 4.6.0Show full stderr[04:43:27] This is snippy 4.6.0
[04:43:27] Written by Torsten Seemann
[04:43:27] Obtained from https://github.com/tseemann/snippy
[04:43:27] Detected operating system: linux
[04:43:27] Enabling bundled linux tools.
[04:43:27] Found bwa - /usr/local/bin/bwa
[04:43:27] Found bcftools - /usr/local/bin/bcftools
[04:43:27] Found samtools - /usr/local/bin/samtools
[04:43:27] Found java - /usr/local/bin/java
[04:43:27] Found snpEff - /usr/local/bin/snpEff
[04:43:27] Found samclip - /usr/local/bin/samclip
[04:43:27] Found seqtk - /usr/local/bin/seqtk
[04:43:27] Found parallel - /usr/local/bin/parallel
[04:43:27] Found freebayes - /usr/local/bin/freebayes
[04:43:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:27] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:27] Found gzip - /bin/gzip
[04:43:27] Found vt - /usr/local/bin/vt
[04:43:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:58] This is snippy 4.6.0Show full stderr[04:43:58] This is snippy 4.6.0
[04:43:58] Written by Torsten Seemann
[04:43:58] Obtained from https://github.com/tseemann/snippy
[04:43:58] Detected operating system: linux
[04:43:58] Enabling bundled linux tools.
[04:43:58] Found bwa - /usr/local/bin/bwa
[04:43:58] Found bcftools - /usr/local/bin/bcftools
[04:43:58] Found samtools - /usr/local/bin/samtools
[04:43:58] Found java - /usr/local/bin/java
[04:43:58] Found snpEff - /usr/local/bin/snpEff
[04:43:58] Found samclip - /usr/local/bin/samclip
[04:43:58] Found seqtk - /usr/local/bin/seqtk
[04:43:58] Found parallel - /usr/local/bin/parallel
[04:43:58] Found freebayes - /usr/local/bin/freebayes
[04:43:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:58] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:58] Found gzip - /bin/gzip
[04:43:58] Found vt - /usr/local/bin/vt
[04:43:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:42:18] This is snippy 4.6.0Show full stderr[04:42:18] This is snippy 4.6.0
[04:42:18] Written by Torsten Seemann
[04:42:18] Obtained from https://github.com/tseemann/snippy
[04:42:18] Detected operating system: linux
[04:42:18] Enabling bundled linux tools.
[04:42:18] Found bwa - /usr/local/bin/bwa
[04:42:18] Found bcftools - /usr/local/bin/bcftools
[04:42:18] Found samtools - /usr/local/bin/samtools
[04:42:18] Found java - /usr/local/bin/java
[04:42:18] Found snpEff - /usr/local/bin/snpEff
[04:42:18] Found samclip - /usr/local/bin/samclip
[04:42:18] Found seqtk - /usr/local/bin/seqtk
[04:42:18] Found parallel - /usr/local/bin/parallel
[04:42:18] Found freebayes - /usr/local/bin/freebayes
[04:42:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:42:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:42:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:42:18] Found vcfuniq - /usr/local/bin/vcfuniq
[04:42:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:42:18] Found gzip - /bin/gzip
[04:42:18] Found vt - /usr/local/bin/vt
[04:42:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:42:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:42:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:42:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:42:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:42:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:42:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:42:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:55:06] This is snippy 4.6.0Show full stderr[04:55:06] This is snippy 4.6.0
[04:55:06] Written by Torsten Seemann
[04:55:06] Obtained from https://github.com/tseemann/snippy
[04:55:06] Detected operating system: linux
[04:55:06] Enabling bundled linux tools.
[04:55:06] Found bwa - /usr/local/bin/bwa
[04:55:06] Found bcftools - /usr/local/bin/bcftools
[04:55:06] Found samtools - /usr/local/bin/samtools
[04:55:06] Found java - /usr/local/bin/java
[04:55:06] Found snpEff - /usr/local/bin/snpEff
[04:55:06] Found samclip - /usr/local/bin/samclip
[04:55:06] Found seqtk - /usr/local/bin/seqtk
[04:55:06] Found parallel - /usr/local/bin/parallel
[04:55:06] Found freebayes - /usr/local/bin/freebayes
[04:55:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:06] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:06] Found gzip - /bin/gzip
[04:55:06] Found vt - /usr/local/bin/vt
[04:55:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:55:21] This is snippy 4.6.0Show full stderr[04:55:21] This is snippy 4.6.0
[04:55:21] Written by Torsten Seemann
[04:55:21] Obtained from https://github.com/tseemann/snippy
[04:55:21] Detected operating system: linux
[04:55:21] Enabling bundled linux tools.
[04:55:21] Found bwa - /usr/local/bin/bwa
[04:55:21] Found bcftools - /usr/local/bin/bcftools
[04:55:21] Found samtools - /usr/local/bin/samtools
[04:55:21] Found java - /usr/local/bin/java
[04:55:21] Found snpEff - /usr/local/bin/snpEff
[04:55:21] Found samclip - /usr/local/bin/samclip
[04:55:21] Found seqtk - /usr/local/bin/seqtk
[04:55:21] Found parallel - /usr/local/bin/parallel
[04:55:21] Found freebayes - /usr/local/bin/freebayes
[04:55:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:21] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:21] Found gzip - /bin/gzip
[04:55:21] Found vt - /usr/local/bin/vt
[04:55:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:55:27] This is snippy 4.6.0Show full stderr[04:55:27] This is snippy 4.6.0
[04:55:27] Written by Torsten Seemann
[04:55:27] Obtained from https://github.com/tseemann/snippy
[04:55:27] Detected operating system: linux
[04:55:27] Enabling bundled linux tools.
[04:55:27] Found bwa - /usr/local/bin/bwa
[04:55:27] Found bcftools - /usr/local/bin/bcftools
[04:55:27] Found samtools - /usr/local/bin/samtools
[04:55:27] Found java - /usr/local/bin/java
[04:55:27] Found snpEff - /usr/local/bin/snpEff
[04:55:27] Found samclip - /usr/local/bin/samclip
[04:55:27] Found seqtk - /usr/local/bin/seqtk
[04:55:27] Found parallel - /usr/local/bin/parallel
[04:55:27] Found freebayes - /usr/local/bin/freebayes
[04:55:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:27] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:27] Found gzip - /bin/gzip
[04:55:27] Found vt - /usr/local/bin/vt
[04:55:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:55:36] This is snippy 4.6.0Show full stderr[04:55:36] This is snippy 4.6.0
[04:55:36] Written by Torsten Seemann
[04:55:36] Obtained from https://github.com/tseemann/snippy
[04:55:36] Detected operating system: linux
[04:55:36] Enabling bundled linux tools.
[04:55:36] Found bwa - /usr/local/bin/bwa
[04:55:36] Found bcftools - /usr/local/bin/bcftools
[04:55:36] Found samtools - /usr/local/bin/samtools
[04:55:36] Found java - /usr/local/bin/java
[04:55:36] Found snpEff - /usr/local/bin/snpEff
[04:55:36] Found samclip - /usr/local/bin/samclip
[04:55:36] Found seqtk - /usr/local/bin/seqtk
[04:55:36] Found parallel - /usr/local/bin/parallel
[04:55:36] Found freebayes - /usr/local/bin/freebayes
[04:55:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:36] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:36] Found gzip - /bin/gzip
[04:55:36] Found vt - /usr/local/bin/vt
[04:55:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:55:43] This is snippy 4.6.0Show full stderr[04:55:43] This is snippy 4.6.0
[04:55:43] Written by Torsten Seemann
[04:55:43] Obtained from https://github.com/tseemann/snippy
[04:55:43] Detected operating system: linux
[04:55:43] Enabling bundled linux tools.
[04:55:43] Found bwa - /usr/local/bin/bwa
[04:55:43] Found bcftools - /usr/local/bin/bcftools
[04:55:43] Found samtools - /usr/local/bin/samtools
[04:55:43] Found java - /usr/local/bin/java
[04:55:43] Found snpEff - /usr/local/bin/snpEff
[04:55:43] Found samclip - /usr/local/bin/samclip
[04:55:43] Found seqtk - /usr/local/bin/seqtk
[04:55:43] Found parallel - /usr/local/bin/parallel
[04:55:43] Found freebayes - /usr/local/bin/freebayes
[04:55:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:43] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:43] Found gzip - /bin/gzip
[04:55:43] Found vt - /usr/local/bin/vt
[04:55:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:56:18] This is snippy 4.6.0Show full stderr[04:56:18] This is snippy 4.6.0
[04:56:18] Written by Torsten Seemann
[04:56:18] Obtained from https://github.com/tseemann/snippy
[04:56:18] Detected operating system: linux
[04:56:18] Enabling bundled linux tools.
[04:56:18] Found bwa - /usr/local/bin/bwa
[04:56:18] Found bcftools - /usr/local/bin/bcftools
[04:56:18] Found samtools - /usr/local/bin/samtools
[04:56:18] Found java - /usr/local/bin/java
[04:56:18] Found snpEff - /usr/local/bin/snpEff
[04:56:18] Found samclip - /usr/local/bin/samclip
[04:56:18] Found seqtk - /usr/local/bin/seqtk
[04:56:18] Found parallel - /usr/local/bin/parallel
[04:56:18] Found freebayes - /usr/local/bin/freebayes
[04:56:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:18] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:18] Found gzip - /bin/gzip
[04:56:18] Found vt - /usr/local/bin/vt
[04:56:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:54:59] This is snippy 4.6.0Show full stderr[04:54:59] This is snippy 4.6.0
[04:54:59] Written by Torsten Seemann
[04:54:59] Obtained from https://github.com/tseemann/snippy
[04:54:59] Detected operating system: linux
[04:54:59] Enabling bundled linux tools.
[04:54:59] Found bwa - /usr/local/bin/bwa
[04:54:59] Found bcftools - /usr/local/bin/bcftools
[04:54:59] Found samtools - /usr/local/bin/samtools
[04:54:59] Found java - /usr/local/bin/java
[04:54:59] Found snpEff - /usr/local/bin/snpEff
[04:54:59] Found samclip - /usr/local/bin/samclip
[04:54:59] Found seqtk - /usr/local/bin/seqtk
[04:54:59] Found parallel - /usr/local/bin/parallel
[04:54:59] Found freebayes - /usr/local/bin/freebayes
[04:54:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:54:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:54:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:54:59] Found vcfuniq - /usr/local/bin/vcfuniq
[04:54:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:54:59] Found gzip - /bin/gzip
[04:54:59] Found vt - /usr/local/bin/vt
[04:54:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:54:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:55:24] This is snippy 4.6.0Show full stderr[04:55:24] This is snippy 4.6.0
[04:55:24] Written by Torsten Seemann
[04:55:24] Obtained from https://github.com/tseemann/snippy
[04:55:24] Detected operating system: linux
[04:55:24] Enabling bundled linux tools.
[04:55:24] Found bwa - /usr/local/bin/bwa
[04:55:24] Found bcftools - /usr/local/bin/bcftools
[04:55:24] Found samtools - /usr/local/bin/samtools
[04:55:24] Found java - /usr/local/bin/java
[04:55:24] Found snpEff - /usr/local/bin/snpEff
[04:55:24] Found samclip - /usr/local/bin/samclip
[04:55:24] Found seqtk - /usr/local/bin/seqtk
[04:55:24] Found parallel - /usr/local/bin/parallel
[04:55:24] Found freebayes - /usr/local/bin/freebayes
[04:55:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:55:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:55:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:55:24] Found vcfuniq - /usr/local/bin/vcfuniq
[04:55:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:55:24] Found gzip - /bin/gzip
[04:55:24] Found vt - /usr/local/bin/vt
[04:55:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:55:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:55:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:55:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:55:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:55:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:55:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:55:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:56:03] This is snippy 4.6.0Show full stderr[04:56:03] This is snippy 4.6.0
[04:56:03] Written by Torsten Seemann
[04:56:03] Obtained from https://github.com/tseemann/snippy
[04:56:03] Detected operating system: linux
[04:56:03] Enabling bundled linux tools.
[04:56:03] Found bwa - /usr/local/bin/bwa
[04:56:03] Found bcftools - /usr/local/bin/bcftools
[04:56:03] Found samtools - /usr/local/bin/samtools
[04:56:03] Found java - /usr/local/bin/java
[04:56:03] Found snpEff - /usr/local/bin/snpEff
[04:56:03] Found samclip - /usr/local/bin/samclip
[04:56:03] Found seqtk - /usr/local/bin/seqtk
[04:56:03] Found parallel - /usr/local/bin/parallel
[04:56:03] Found freebayes - /usr/local/bin/freebayes
[04:56:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:03] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:03] Found gzip - /bin/gzip
[04:56:03] Found vt - /usr/local/bin/vt
[04:56:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:56:06] This is snippy 4.6.0Show full stderr[04:56:06] This is snippy 4.6.0
[04:56:06] Written by Torsten Seemann
[04:56:06] Obtained from https://github.com/tseemann/snippy
[04:56:06] Detected operating system: linux
[04:56:06] Enabling bundled linux tools.
[04:56:06] Found bwa - /usr/local/bin/bwa
[04:56:06] Found bcftools - /usr/local/bin/bcftools
[04:56:06] Found samtools - /usr/local/bin/samtools
[04:56:06] Found java - /usr/local/bin/java
[04:56:06] Found snpEff - /usr/local/bin/snpEff
[04:56:06] Found samclip - /usr/local/bin/samclip
[04:56:06] Found seqtk - /usr/local/bin/seqtk
[04:56:06] Found parallel - /usr/local/bin/parallel
[04:56:06] Found freebayes - /usr/local/bin/freebayes
[04:56:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:06] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:06] Found gzip - /bin/gzip
[04:56:06] Found vt - /usr/local/bin/vt
[04:56:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:56:24] This is snippy 4.6.0Show full stderr[04:56:24] This is snippy 4.6.0
[04:56:24] Written by Torsten Seemann
[04:56:24] Obtained from https://github.com/tseemann/snippy
[04:56:24] Detected operating system: linux
[04:56:24] Enabling bundled linux tools.
[04:56:24] Found bwa - /usr/local/bin/bwa
[04:56:24] Found bcftools - /usr/local/bin/bcftools
[04:56:24] Found samtools - /usr/local/bin/samtools
[04:56:24] Found java - /usr/local/bin/java
[04:56:24] Found snpEff - /usr/local/bin/snpEff
[04:56:24] Found samclip - /usr/local/bin/samclip
[04:56:24] Found seqtk - /usr/local/bin/seqtk
[04:56:24] Found parallel - /usr/local/bin/parallel
[04:56:24] Found freebayes - /usr/local/bin/freebayes
[04:56:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:24] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:24] Found gzip - /bin/gzip
[04:56:24] Found vt - /usr/local/bin/vt
[04:56:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:57:57] This is snippy 4.6.0Show full stderr[04:57:57] This is snippy 4.6.0
[04:57:57] Written by Torsten Seemann
[04:57:57] Obtained from https://github.com/tseemann/snippy
[04:57:57] Detected operating system: linux
[04:57:57] Enabling bundled linux tools.
[04:57:57] Found bwa - /usr/local/bin/bwa
[04:57:57] Found bcftools - /usr/local/bin/bcftools
[04:57:57] Found samtools - /usr/local/bin/samtools
[04:57:57] Found java - /usr/local/bin/java
[04:57:57] Found snpEff - /usr/local/bin/snpEff
[04:57:57] Found samclip - /usr/local/bin/samclip
[04:57:57] Found seqtk - /usr/local/bin/seqtk
[04:57:57] Found parallel - /usr/local/bin/parallel
[04:57:57] Found freebayes - /usr/local/bin/freebayes
[04:57:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:57] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:57] Found gzip - /bin/gzip
[04:57:57] Found vt - /usr/local/bin/vt
[04:57:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:57:12] This is snippy 4.6.0Show full stderr[04:57:12] This is snippy 4.6.0
[04:57:12] Written by Torsten Seemann
[04:57:12] Obtained from https://github.com/tseemann/snippy
[04:57:12] Detected operating system: linux
[04:57:12] Enabling bundled linux tools.
[04:57:12] Found bwa - /usr/local/bin/bwa
[04:57:12] Found bcftools - /usr/local/bin/bcftools
[04:57:12] Found samtools - /usr/local/bin/samtools
[04:57:12] Found java - /usr/local/bin/java
[04:57:12] Found snpEff - /usr/local/bin/snpEff
[04:57:12] Found samclip - /usr/local/bin/samclip
[04:57:12] Found seqtk - /usr/local/bin/seqtk
[04:57:12] Found parallel - /usr/local/bin/parallel
[04:57:12] Found freebayes - /usr/local/bin/freebayes
[04:57:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:12] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:12] Found gzip - /bin/gzip
[04:57:12] Found vt - /usr/local/bin/vt
[04:57:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:59:00] This is snippy 4.6.0Show full stderr[04:59:00] This is snippy 4.6.0
[04:59:00] Written by Torsten Seemann
[04:59:00] Obtained from https://github.com/tseemann/snippy
[04:59:00] Detected operating system: linux
[04:59:00] Enabling bundled linux tools.
[04:59:00] Found bwa - /usr/local/bin/bwa
[04:59:00] Found bcftools - /usr/local/bin/bcftools
[04:59:00] Found samtools - /usr/local/bin/samtools
[04:59:00] Found java - /usr/local/bin/java
[04:59:00] Found snpEff - /usr/local/bin/snpEff
[04:59:00] Found samclip - /usr/local/bin/samclip
[04:59:00] Found seqtk - /usr/local/bin/seqtk
[04:59:00] Found parallel - /usr/local/bin/parallel
[04:59:00] Found freebayes - /usr/local/bin/freebayes
[04:59:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:00] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:00] Found gzip - /bin/gzip
[04:59:00] Found vt - /usr/local/bin/vt
[04:59:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:59:21] This is snippy 4.6.0Show full stderr[04:59:21] This is snippy 4.6.0
[04:59:21] Written by Torsten Seemann
[04:59:21] Obtained from https://github.com/tseemann/snippy
[04:59:21] Detected operating system: linux
[04:59:21] Enabling bundled linux tools.
[04:59:21] Found bwa - /usr/local/bin/bwa
[04:59:21] Found bcftools - /usr/local/bin/bcftools
[04:59:21] Found samtools - /usr/local/bin/samtools
[04:59:21] Found java - /usr/local/bin/java
[04:59:21] Found snpEff - /usr/local/bin/snpEff
[04:59:21] Found samclip - /usr/local/bin/samclip
[04:59:21] Found seqtk - /usr/local/bin/seqtk
[04:59:21] Found parallel - /usr/local/bin/parallel
[04:59:21] Found freebayes - /usr/local/bin/freebayes
[04:59:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:21] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:21] Found gzip - /bin/gzip
[04:59:21] Found vt - /usr/local/bin/vt
[04:59:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:57:15] This is snippy 4.6.0Show full stderr[04:57:15] This is snippy 4.6.0
[04:57:15] Written by Torsten Seemann
[04:57:15] Obtained from https://github.com/tseemann/snippy
[04:57:15] Detected operating system: linux
[04:57:15] Enabling bundled linux tools.
[04:57:15] Found bwa - /usr/local/bin/bwa
[04:57:15] Found bcftools - /usr/local/bin/bcftools
[04:57:15] Found samtools - /usr/local/bin/samtools
[04:57:15] Found java - /usr/local/bin/java
[04:57:15] Found snpEff - /usr/local/bin/snpEff
[04:57:15] Found samclip - /usr/local/bin/samclip
[04:57:15] Found seqtk - /usr/local/bin/seqtk
[04:57:15] Found parallel - /usr/local/bin/parallel
[04:57:15] Found freebayes - /usr/local/bin/freebayes
[04:57:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:15] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:15] Found gzip - /bin/gzip
[04:57:15] Found vt - /usr/local/bin/vt
[04:57:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:57:27] This is snippy 4.6.0Show full stderr[04:57:27] This is snippy 4.6.0
[04:57:27] Written by Torsten Seemann
[04:57:27] Obtained from https://github.com/tseemann/snippy
[04:57:27] Detected operating system: linux
[04:57:27] Enabling bundled linux tools.
[04:57:27] Found bwa - /usr/local/bin/bwa
[04:57:27] Found bcftools - /usr/local/bin/bcftools
[04:57:27] Found samtools - /usr/local/bin/samtools
[04:57:27] Found java - /usr/local/bin/java
[04:57:27] Found snpEff - /usr/local/bin/snpEff
[04:57:27] Found samclip - /usr/local/bin/samclip
[04:57:27] Found seqtk - /usr/local/bin/seqtk
[04:57:27] Found parallel - /usr/local/bin/parallel
[04:57:27] Found freebayes - /usr/local/bin/freebayes
[04:57:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:27] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:27] Found gzip - /bin/gzip
[04:57:27] Found vt - /usr/local/bin/vt
[04:57:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:57:42] This is snippy 4.6.0Show full stderr[04:57:42] This is snippy 4.6.0
[04:57:42] Written by Torsten Seemann
[04:57:42] Obtained from https://github.com/tseemann/snippy
[04:57:42] Detected operating system: linux
[04:57:42] Enabling bundled linux tools.
[04:57:42] Found bwa - /usr/local/bin/bwa
[04:57:42] Found bcftools - /usr/local/bin/bcftools
[04:57:42] Found samtools - /usr/local/bin/samtools
[04:57:42] Found java - /usr/local/bin/java
[04:57:42] Found snpEff - /usr/local/bin/snpEff
[04:57:42] Found samclip - /usr/local/bin/samclip
[04:57:42] Found seqtk - /usr/local/bin/seqtk
[04:57:42] Found parallel - /usr/local/bin/parallel
[04:57:42] Found freebayes - /usr/local/bin/freebayes
[04:57:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:57:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:57:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:57:42] Found vcfuniq - /usr/local/bin/vcfuniq
[04:57:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:57:42] Found gzip - /bin/gzip
[04:57:42] Found vt - /usr/local/bin/vt
[04:57:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:57:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:57:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:57:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:57:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:57:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:57:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:57:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:58:36] This is snippy 4.6.0Show full stderr[04:58:36] This is snippy 4.6.0
[04:58:36] Written by Torsten Seemann
[04:58:36] Obtained from https://github.com/tseemann/snippy
[04:58:36] Detected operating system: linux
[04:58:36] Enabling bundled linux tools.
[04:58:36] Found bwa - /usr/local/bin/bwa
[04:58:36] Found bcftools - /usr/local/bin/bcftools
[04:58:36] Found samtools - /usr/local/bin/samtools
[04:58:36] Found java - /usr/local/bin/java
[04:58:36] Found snpEff - /usr/local/bin/snpEff
[04:58:36] Found samclip - /usr/local/bin/samclip
[04:58:36] Found seqtk - /usr/local/bin/seqtk
[04:58:36] Found parallel - /usr/local/bin/parallel
[04:58:36] Found freebayes - /usr/local/bin/freebayes
[04:58:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:58:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:58:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:58:36] Found vcfuniq - /usr/local/bin/vcfuniq
[04:58:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:58:36] Found gzip - /bin/gzip
[04:58:36] Found vt - /usr/local/bin/vt
[04:58:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:58:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:58:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:58:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:58:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:58:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:58:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:58:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:59:36] This is snippy 4.6.0Show full stderr[04:59:36] This is snippy 4.6.0
[04:59:36] Written by Torsten Seemann
[04:59:36] Obtained from https://github.com/tseemann/snippy
[04:59:36] Detected operating system: linux
[04:59:36] Enabling bundled linux tools.
[04:59:36] Found bwa - /usr/local/bin/bwa
[04:59:36] Found bcftools - /usr/local/bin/bcftools
[04:59:36] Found samtools - /usr/local/bin/samtools
[04:59:36] Found java - /usr/local/bin/java
[04:59:37] Found snpEff - /usr/local/bin/snpEff
[04:59:37] Found samclip - /usr/local/bin/samclip
[04:59:37] Found seqtk - /usr/local/bin/seqtk
[04:59:37] Found parallel - /usr/local/bin/parallel
[04:59:37] Found freebayes - /usr/local/bin/freebayes
[04:59:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:37] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:37] Found gzip - /bin/gzip
[04:59:37] Found vt - /usr/local/bin/vt
[04:59:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:06] This is snippy 4.6.0Show full stderr[05:00:06] This is snippy 4.6.0
[05:00:06] Written by Torsten Seemann
[05:00:06] Obtained from https://github.com/tseemann/snippy
[05:00:06] Detected operating system: linux
[05:00:06] Enabling bundled linux tools.
[05:00:06] Found bwa - /usr/local/bin/bwa
[05:00:06] Found bcftools - /usr/local/bin/bcftools
[05:00:06] Found samtools - /usr/local/bin/samtools
[05:00:06] Found java - /usr/local/bin/java
[05:00:06] Found snpEff - /usr/local/bin/snpEff
[05:00:06] Found samclip - /usr/local/bin/samclip
[05:00:06] Found seqtk - /usr/local/bin/seqtk
[05:00:06] Found parallel - /usr/local/bin/parallel
[05:00:06] Found freebayes - /usr/local/bin/freebayes
[05:00:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:06] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:06] Found gzip - /bin/gzip
[05:00:06] Found vt - /usr/local/bin/vt
[05:00:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:09] This is snippy 4.6.0Show full stderr[05:00:09] This is snippy 4.6.0
[05:00:09] Written by Torsten Seemann
[05:00:09] Obtained from https://github.com/tseemann/snippy
[05:00:09] Detected operating system: linux
[05:00:09] Enabling bundled linux tools.
[05:00:09] Found bwa - /usr/local/bin/bwa
[05:00:09] Found bcftools - /usr/local/bin/bcftools
[05:00:09] Found samtools - /usr/local/bin/samtools
[05:00:09] Found java - /usr/local/bin/java
[05:00:09] Found snpEff - /usr/local/bin/snpEff
[05:00:09] Found samclip - /usr/local/bin/samclip
[05:00:09] Found seqtk - /usr/local/bin/seqtk
[05:00:09] Found parallel - /usr/local/bin/parallel
[05:00:09] Found freebayes - /usr/local/bin/freebayes
[05:00:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:09] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:09] Found gzip - /bin/gzip
[05:00:09] Found vt - /usr/local/bin/vt
[05:00:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:05] This is snippy 4.6.0Show full stderr[05:01:05] This is snippy 4.6.0
[05:01:05] Written by Torsten Seemann
[05:01:05] Obtained from https://github.com/tseemann/snippy
[05:01:05] Detected operating system: linux
[05:01:05] Enabling bundled linux tools.
[05:01:05] Found bwa - /usr/local/bin/bwa
[05:01:05] Found bcftools - /usr/local/bin/bcftools
[05:01:05] Found samtools - /usr/local/bin/samtools
[05:01:05] Found java - /usr/local/bin/java
[05:01:05] Found snpEff - /usr/local/bin/snpEff
[05:01:05] Found samclip - /usr/local/bin/samclip
[05:01:05] Found seqtk - /usr/local/bin/seqtk
[05:01:05] Found parallel - /usr/local/bin/parallel
[05:01:05] Found freebayes - /usr/local/bin/freebayes
[05:01:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:05] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:05] Found gzip - /bin/gzip
[05:01:06] Found vt - /usr/local/bin/vt
[05:01:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:16] This is snippy 4.6.0Show full stderr[05:01:16] This is snippy 4.6.0
[05:01:16] Written by Torsten Seemann
[05:01:16] Obtained from https://github.com/tseemann/snippy
[05:01:16] Detected operating system: linux
[05:01:16] Enabling bundled linux tools.
[05:01:16] Found bwa - /usr/local/bin/bwa
[05:01:16] Found bcftools - /usr/local/bin/bcftools
[05:01:16] Found samtools - /usr/local/bin/samtools
[05:01:16] Found java - /usr/local/bin/java
[05:01:16] Found snpEff - /usr/local/bin/snpEff
[05:01:16] Found samclip - /usr/local/bin/samclip
[05:01:16] Found seqtk - /usr/local/bin/seqtk
[05:01:16] Found parallel - /usr/local/bin/parallel
[05:01:16] Found freebayes - /usr/local/bin/freebayes
[05:01:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:16] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:16] Found gzip - /bin/gzip
[05:01:16] Found vt - /usr/local/bin/vt
[05:01:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:56:36] This is snippy 4.6.0Show full stderr[04:56:36] This is snippy 4.6.0
[04:56:36] Written by Torsten Seemann
[04:56:36] Obtained from https://github.com/tseemann/snippy
[04:56:36] Detected operating system: linux
[04:56:36] Enabling bundled linux tools.
[04:56:36] Found bwa - /usr/local/bin/bwa
[04:56:36] Found bcftools - /usr/local/bin/bcftools
[04:56:36] Found samtools - /usr/local/bin/samtools
[04:56:36] Found java - /usr/local/bin/java
[04:56:36] Found snpEff - /usr/local/bin/snpEff
[04:56:36] Found samclip - /usr/local/bin/samclip
[04:56:36] Found seqtk - /usr/local/bin/seqtk
[04:56:36] Found parallel - /usr/local/bin/parallel
[04:56:36] Found freebayes - /usr/local/bin/freebayes
[04:56:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:56:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:56:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:56:36] Found vcfuniq - /usr/local/bin/vcfuniq
[04:56:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:56:36] Found gzip - /bin/gzip
[04:56:36] Found vt - /usr/local/bin/vt
[04:56:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:56:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:56:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:56:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:56:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:56:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:56:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:56:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:58:30] This is snippy 4.6.0Show full stderr[04:58:30] This is snippy 4.6.0
[04:58:30] Written by Torsten Seemann
[04:58:30] Obtained from https://github.com/tseemann/snippy
[04:58:30] Detected operating system: linux
[04:58:30] Enabling bundled linux tools.
[04:58:30] Found bwa - /usr/local/bin/bwa
[04:58:30] Found bcftools - /usr/local/bin/bcftools
[04:58:30] Found samtools - /usr/local/bin/samtools
[04:58:30] Found java - /usr/local/bin/java
[04:58:30] Found snpEff - /usr/local/bin/snpEff
[04:58:30] Found samclip - /usr/local/bin/samclip
[04:58:30] Found seqtk - /usr/local/bin/seqtk
[04:58:30] Found parallel - /usr/local/bin/parallel
[04:58:30] Found freebayes - /usr/local/bin/freebayes
[04:58:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:58:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:58:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:58:30] Found vcfuniq - /usr/local/bin/vcfuniq
[04:58:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:58:30] Found gzip - /bin/gzip
[04:58:30] Found vt - /usr/local/bin/vt
[04:58:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:58:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:58:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:58:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:58:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:58:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:58:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:58:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:18] This is snippy 4.6.0Show full stderr[05:00:18] This is snippy 4.6.0
[05:00:18] Written by Torsten Seemann
[05:00:18] Obtained from https://github.com/tseemann/snippy
[05:00:18] Detected operating system: linux
[05:00:18] Enabling bundled linux tools.
[05:00:18] Found bwa - /usr/local/bin/bwa
[05:00:18] Found bcftools - /usr/local/bin/bcftools
[05:00:18] Found samtools - /usr/local/bin/samtools
[05:00:18] Found java - /usr/local/bin/java
[05:00:18] Found snpEff - /usr/local/bin/snpEff
[05:00:18] Found samclip - /usr/local/bin/samclip
[05:00:18] Found seqtk - /usr/local/bin/seqtk
[05:00:18] Found parallel - /usr/local/bin/parallel
[05:00:18] Found freebayes - /usr/local/bin/freebayes
[05:00:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:18] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:18] Found gzip - /bin/gzip
[05:00:18] Found vt - /usr/local/bin/vt
[05:00:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:20] This is snippy 4.6.0Show full stderr[05:00:20] This is snippy 4.6.0
[05:00:20] Written by Torsten Seemann
[05:00:20] Obtained from https://github.com/tseemann/snippy
[05:00:20] Detected operating system: linux
[05:00:20] Enabling bundled linux tools.
[05:00:20] Found bwa - /usr/local/bin/bwa
[05:00:20] Found bcftools - /usr/local/bin/bcftools
[05:00:20] Found samtools - /usr/local/bin/samtools
[05:00:20] Found java - /usr/local/bin/java
[05:00:20] Found snpEff - /usr/local/bin/snpEff
[05:00:20] Found samclip - /usr/local/bin/samclip
[05:00:20] Found seqtk - /usr/local/bin/seqtk
[05:00:20] Found parallel - /usr/local/bin/parallel
[05:00:20] Found freebayes - /usr/local/bin/freebayes
[05:00:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:20] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:20] Found gzip - /bin/gzip
[05:00:20] Found vt - /usr/local/bin/vt
[05:00:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:33] This is snippy 4.6.0Show full stderr[05:00:33] This is snippy 4.6.0
[05:00:33] Written by Torsten Seemann
[05:00:33] Obtained from https://github.com/tseemann/snippy
[05:00:33] Detected operating system: linux
[05:00:33] Enabling bundled linux tools.
[05:00:33] Found bwa - /usr/local/bin/bwa
[05:00:33] Found bcftools - /usr/local/bin/bcftools
[05:00:33] Found samtools - /usr/local/bin/samtools
[05:00:33] Found java - /usr/local/bin/java
[05:00:33] Found snpEff - /usr/local/bin/snpEff
[05:00:33] Found samclip - /usr/local/bin/samclip
[05:00:33] Found seqtk - /usr/local/bin/seqtk
[05:00:33] Found parallel - /usr/local/bin/parallel
[05:00:33] Found freebayes - /usr/local/bin/freebayes
[05:00:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:33] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:33] Found gzip - /bin/gzip
[05:00:33] Found vt - /usr/local/bin/vt
[05:00:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:02] This is snippy 4.6.0Show full stderr[05:01:02] This is snippy 4.6.0
[05:01:02] Written by Torsten Seemann
[05:01:02] Obtained from https://github.com/tseemann/snippy
[05:01:02] Detected operating system: linux
[05:01:02] Enabling bundled linux tools.
[05:01:02] Found bwa - /usr/local/bin/bwa
[05:01:02] Found bcftools - /usr/local/bin/bcftools
[05:01:02] Found samtools - /usr/local/bin/samtools
[05:01:02] Found java - /usr/local/bin/java
[05:01:02] Found snpEff - /usr/local/bin/snpEff
[05:01:02] Found samclip - /usr/local/bin/samclip
[05:01:02] Found seqtk - /usr/local/bin/seqtk
[05:01:02] Found parallel - /usr/local/bin/parallel
[05:01:02] Found freebayes - /usr/local/bin/freebayes
[05:01:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:02] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:02] Found gzip - /bin/gzip
[05:01:02] Found vt - /usr/local/bin/vt
[05:01:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:18] This is snippy 4.6.0Show full stderr[05:01:18] This is snippy 4.6.0
[05:01:18] Written by Torsten Seemann
[05:01:18] Obtained from https://github.com/tseemann/snippy
[05:01:18] Detected operating system: linux
[05:01:18] Enabling bundled linux tools.
[05:01:18] Found bwa - /usr/local/bin/bwa
[05:01:18] Found bcftools - /usr/local/bin/bcftools
[05:01:18] Found samtools - /usr/local/bin/samtools
[05:01:19] Found java - /usr/local/bin/java
[05:01:19] Found snpEff - /usr/local/bin/snpEff
[05:01:19] Found samclip - /usr/local/bin/samclip
[05:01:19] Found seqtk - /usr/local/bin/seqtk
[05:01:19] Found parallel - /usr/local/bin/parallel
[05:01:19] Found freebayes - /usr/local/bin/freebayes
[05:01:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:19] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:19] Found gzip - /bin/gzip
[05:01:19] Found vt - /usr/local/bin/vt
[05:01:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:27] This is snippy 4.6.0Show full stderr[05:01:27] This is snippy 4.6.0
[05:01:27] Written by Torsten Seemann
[05:01:27] Obtained from https://github.com/tseemann/snippy
[05:01:27] Detected operating system: linux
[05:01:27] Enabling bundled linux tools.
[05:01:27] Found bwa - /usr/local/bin/bwa
[05:01:27] Found bcftools - /usr/local/bin/bcftools
[05:01:27] Found samtools - /usr/local/bin/samtools
[05:01:27] Found java - /usr/local/bin/java
[05:01:27] Found snpEff - /usr/local/bin/snpEff
[05:01:27] Found samclip - /usr/local/bin/samclip
[05:01:27] Found seqtk - /usr/local/bin/seqtk
[05:01:27] Found parallel - /usr/local/bin/parallel
[05:01:27] Found freebayes - /usr/local/bin/freebayes
[05:01:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:27] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:27] Found gzip - /bin/gzip
[05:01:27] Found vt - /usr/local/bin/vt
[05:01:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:42] This is snippy 4.6.0Show full stderr[05:01:42] This is snippy 4.6.0
[05:01:42] Written by Torsten Seemann
[05:01:42] Obtained from https://github.com/tseemann/snippy
[05:01:42] Detected operating system: linux
[05:01:42] Enabling bundled linux tools.
[05:01:42] Found bwa - /usr/local/bin/bwa
[05:01:42] Found bcftools - /usr/local/bin/bcftools
[05:01:42] Found samtools - /usr/local/bin/samtools
[05:01:42] Found java - /usr/local/bin/java
[05:01:42] Found snpEff - /usr/local/bin/snpEff
[05:01:42] Found samclip - /usr/local/bin/samclip
[05:01:42] Found seqtk - /usr/local/bin/seqtk
[05:01:42] Found parallel - /usr/local/bin/parallel
[05:01:42] Found freebayes - /usr/local/bin/freebayes
[05:01:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:42] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:42] Found gzip - /bin/gzip
[05:01:42] Found vt - /usr/local/bin/vt
[05:01:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:43] This is snippy 4.6.0Show full stderr[05:01:43] This is snippy 4.6.0
[05:01:43] Written by Torsten Seemann
[05:01:43] Obtained from https://github.com/tseemann/snippy
[05:01:43] Detected operating system: linux
[05:01:43] Enabling bundled linux tools.
[05:01:43] Found bwa - /usr/local/bin/bwa
[05:01:44] Found bcftools - /usr/local/bin/bcftools
[05:01:44] Found samtools - /usr/local/bin/samtools
[05:01:44] Found java - /usr/local/bin/java
[05:01:44] Found snpEff - /usr/local/bin/snpEff
[05:01:44] Found samclip - /usr/local/bin/samclip
[05:01:44] Found seqtk - /usr/local/bin/seqtk
[05:01:44] Found parallel - /usr/local/bin/parallel
[05:01:44] Found freebayes - /usr/local/bin/freebayes
[05:01:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:44] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:44] Found gzip - /bin/gzip
[05:01:44] Found vt - /usr/local/bin/vt
[05:01:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:55] This is snippy 4.6.0Show full stderr[05:01:55] This is snippy 4.6.0
[05:01:55] Written by Torsten Seemann
[05:01:55] Obtained from https://github.com/tseemann/snippy
[05:01:55] Detected operating system: linux
[05:01:55] Enabling bundled linux tools.
[05:01:55] Found bwa - /usr/local/bin/bwa
[05:01:55] Found bcftools - /usr/local/bin/bcftools
[05:01:55] Found samtools - /usr/local/bin/samtools
[05:01:55] Found java - /usr/local/bin/java
[05:01:55] Found snpEff - /usr/local/bin/snpEff
[05:01:55] Found samclip - /usr/local/bin/samclip
[05:01:55] Found seqtk - /usr/local/bin/seqtk
[05:01:55] Found parallel - /usr/local/bin/parallel
[05:01:55] Found freebayes - /usr/local/bin/freebayes
[05:01:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:55] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:56] Found gzip - /bin/gzip
[05:01:56] Found vt - /usr/local/bin/vt
[05:01:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:02:12] This is snippy 4.6.0Show full stderr[05:02:12] This is snippy 4.6.0
[05:02:12] Written by Torsten Seemann
[05:02:12] Obtained from https://github.com/tseemann/snippy
[05:02:12] Detected operating system: linux
[05:02:12] Enabling bundled linux tools.
[05:02:12] Found bwa - /usr/local/bin/bwa
[05:02:12] Found bcftools - /usr/local/bin/bcftools
[05:02:12] Found samtools - /usr/local/bin/samtools
[05:02:12] Found java - /usr/local/bin/java
[05:02:12] Found snpEff - /usr/local/bin/snpEff
[05:02:12] Found samclip - /usr/local/bin/samclip
[05:02:12] Found seqtk - /usr/local/bin/seqtk
[05:02:12] Found parallel - /usr/local/bin/parallel
[05:02:12] Found freebayes - /usr/local/bin/freebayes
[05:02:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:12] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:13] Found gzip - /bin/gzip
[05:02:13] Found vt - /usr/local/bin/vt
[05:02:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:46] This is snippy 4.6.0Show full stderr[05:01:46] This is snippy 4.6.0
[05:01:46] Written by Torsten Seemann
[05:01:46] Obtained from https://github.com/tseemann/snippy
[05:01:46] Detected operating system: linux
[05:01:46] Enabling bundled linux tools.
[05:01:46] Found bwa - /usr/local/bin/bwa
[05:01:46] Found bcftools - /usr/local/bin/bcftools
[05:01:46] Found samtools - /usr/local/bin/samtools
[05:01:46] Found java - /usr/local/bin/java
[05:01:46] Found snpEff - /usr/local/bin/snpEff
[05:01:46] Found samclip - /usr/local/bin/samclip
[05:01:46] Found seqtk - /usr/local/bin/seqtk
[05:01:46] Found parallel - /usr/local/bin/parallel
[05:01:46] Found freebayes - /usr/local/bin/freebayes
[05:01:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:47] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:47] Found gzip - /bin/gzip
[05:01:47] Found vt - /usr/local/bin/vt
[05:01:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:58:45] This is snippy 4.6.0Show full stderr[04:58:45] This is snippy 4.6.0
[04:58:45] Written by Torsten Seemann
[04:58:45] Obtained from https://github.com/tseemann/snippy
[04:58:45] Detected operating system: linux
[04:58:45] Enabling bundled linux tools.
[04:58:45] Found bwa - /usr/local/bin/bwa
[04:58:45] Found bcftools - /usr/local/bin/bcftools
[04:58:45] Found samtools - /usr/local/bin/samtools
[04:58:45] Found java - /usr/local/bin/java
[04:58:45] Found snpEff - /usr/local/bin/snpEff
[04:58:45] Found samclip - /usr/local/bin/samclip
[04:58:45] Found seqtk - /usr/local/bin/seqtk
[04:58:45] Found parallel - /usr/local/bin/parallel
[04:58:45] Found freebayes - /usr/local/bin/freebayes
[04:58:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:58:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:58:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:58:45] Found vcfuniq - /usr/local/bin/vcfuniq
[04:58:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:58:45] Found gzip - /bin/gzip
[04:58:45] Found vt - /usr/local/bin/vt
[04:58:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:58:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:58:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:58:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:58:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:58:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:58:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:58:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:59:15] This is snippy 4.6.0Show full stderr[04:59:15] This is snippy 4.6.0
[04:59:15] Written by Torsten Seemann
[04:59:15] Obtained from https://github.com/tseemann/snippy
[04:59:15] Detected operating system: linux
[04:59:15] Enabling bundled linux tools.
[04:59:15] Found bwa - /usr/local/bin/bwa
[04:59:15] Found bcftools - /usr/local/bin/bcftools
[04:59:15] Found samtools - /usr/local/bin/samtools
[04:59:15] Found java - /usr/local/bin/java
[04:59:15] Found snpEff - /usr/local/bin/snpEff
[04:59:15] Found samclip - /usr/local/bin/samclip
[04:59:15] Found seqtk - /usr/local/bin/seqtk
[04:59:15] Found parallel - /usr/local/bin/parallel
[04:59:15] Found freebayes - /usr/local/bin/freebayes
[04:59:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:15] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:15] Found gzip - /bin/gzip
[04:59:15] Found vt - /usr/local/bin/vt
[04:59:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:59:27] This is snippy 4.6.0Show full stderr[04:59:27] This is snippy 4.6.0
[04:59:27] Written by Torsten Seemann
[04:59:27] Obtained from https://github.com/tseemann/snippy
[04:59:27] Detected operating system: linux
[04:59:27] Enabling bundled linux tools.
[04:59:27] Found bwa - /usr/local/bin/bwa
[04:59:27] Found bcftools - /usr/local/bin/bcftools
[04:59:27] Found samtools - /usr/local/bin/samtools
[04:59:27] Found java - /usr/local/bin/java
[04:59:27] Found snpEff - /usr/local/bin/snpEff
[04:59:27] Found samclip - /usr/local/bin/samclip
[04:59:27] Found seqtk - /usr/local/bin/seqtk
[04:59:27] Found parallel - /usr/local/bin/parallel
[04:59:27] Found freebayes - /usr/local/bin/freebayes
[04:59:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:27] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:27] Found gzip - /bin/gzip
[04:59:27] Found vt - /usr/local/bin/vt
[04:59:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:59:30] This is snippy 4.6.0Show full stderr[04:59:30] This is snippy 4.6.0
[04:59:30] Written by Torsten Seemann
[04:59:30] Obtained from https://github.com/tseemann/snippy
[04:59:30] Detected operating system: linux
[04:59:30] Enabling bundled linux tools.
[04:59:30] Found bwa - /usr/local/bin/bwa
[04:59:30] Found bcftools - /usr/local/bin/bcftools
[04:59:30] Found samtools - /usr/local/bin/samtools
[04:59:30] Found java - /usr/local/bin/java
[04:59:30] Found snpEff - /usr/local/bin/snpEff
[04:59:30] Found samclip - /usr/local/bin/samclip
[04:59:30] Found seqtk - /usr/local/bin/seqtk
[04:59:30] Found parallel - /usr/local/bin/parallel
[04:59:30] Found freebayes - /usr/local/bin/freebayes
[04:59:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:30] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:30] Found gzip - /bin/gzip
[04:59:30] Found vt - /usr/local/bin/vt
[04:59:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:59:45] This is snippy 4.6.0Show full stderr[04:59:45] This is snippy 4.6.0
[04:59:45] Written by Torsten Seemann
[04:59:45] Obtained from https://github.com/tseemann/snippy
[04:59:45] Detected operating system: linux
[04:59:45] Enabling bundled linux tools.
[04:59:45] Found bwa - /usr/local/bin/bwa
[04:59:45] Found bcftools - /usr/local/bin/bcftools
[04:59:45] Found samtools - /usr/local/bin/samtools
[04:59:45] Found java - /usr/local/bin/java
[04:59:45] Found snpEff - /usr/local/bin/snpEff
[04:59:45] Found samclip - /usr/local/bin/samclip
[04:59:45] Found seqtk - /usr/local/bin/seqtk
[04:59:45] Found parallel - /usr/local/bin/parallel
[04:59:45] Found freebayes - /usr/local/bin/freebayes
[04:59:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:45] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:46] Found gzip - /bin/gzip
[04:59:46] Found vt - /usr/local/bin/vt
[04:59:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:58] This is snippy 4.6.0Show full stderr[05:01:58] This is snippy 4.6.0
[05:01:58] Written by Torsten Seemann
[05:01:58] Obtained from https://github.com/tseemann/snippy
[05:01:58] Detected operating system: linux
[05:01:58] Enabling bundled linux tools.
[05:01:58] Found bwa - /usr/local/bin/bwa
[05:01:59] Found bcftools - /usr/local/bin/bcftools
[05:01:59] Found samtools - /usr/local/bin/samtools
[05:01:59] Found java - /usr/local/bin/java
[05:01:59] Found snpEff - /usr/local/bin/snpEff
[05:01:59] Found samclip - /usr/local/bin/samclip
[05:01:59] Found seqtk - /usr/local/bin/seqtk
[05:01:59] Found parallel - /usr/local/bin/parallel
[05:01:59] Found freebayes - /usr/local/bin/freebayes
[05:01:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:59] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:59] Found gzip - /bin/gzip
[05:01:59] Found vt - /usr/local/bin/vt
[05:01:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:02:02] This is snippy 4.6.0Show full stderr[05:02:02] This is snippy 4.6.0
[05:02:02] Written by Torsten Seemann
[05:02:02] Obtained from https://github.com/tseemann/snippy
[05:02:02] Detected operating system: linux
[05:02:02] Enabling bundled linux tools.
[05:02:02] Found bwa - /usr/local/bin/bwa
[05:02:02] Found bcftools - /usr/local/bin/bcftools
[05:02:02] Found samtools - /usr/local/bin/samtools
[05:02:02] Found java - /usr/local/bin/java
[05:02:02] Found snpEff - /usr/local/bin/snpEff
[05:02:02] Found samclip - /usr/local/bin/samclip
[05:02:02] Found seqtk - /usr/local/bin/seqtk
[05:02:02] Found parallel - /usr/local/bin/parallel
[05:02:02] Found freebayes - /usr/local/bin/freebayes
[05:02:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:02] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:02] Found gzip - /bin/gzip
[05:02:02] Found vt - /usr/local/bin/vt
[05:02:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:02:03] This is snippy 4.6.0Show full stderr[05:02:03] This is snippy 4.6.0
[05:02:03] Written by Torsten Seemann
[05:02:03] Obtained from https://github.com/tseemann/snippy
[05:02:03] Detected operating system: linux
[05:02:03] Enabling bundled linux tools.
[05:02:03] Found bwa - /usr/local/bin/bwa
[05:02:03] Found bcftools - /usr/local/bin/bcftools
[05:02:03] Found samtools - /usr/local/bin/samtools
[05:02:03] Found java - /usr/local/bin/java
[05:02:03] Found snpEff - /usr/local/bin/snpEff
[05:02:03] Found samclip - /usr/local/bin/samclip
[05:02:03] Found seqtk - /usr/local/bin/seqtk
[05:02:03] Found parallel - /usr/local/bin/parallel
[05:02:03] Found freebayes - /usr/local/bin/freebayes
[05:02:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:03] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:03] Found gzip - /bin/gzip
[05:02:03] Found vt - /usr/local/bin/vt
[05:02:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:03:10] This is snippy 4.6.0Show full stderr[05:03:10] This is snippy 4.6.0
[05:03:10] Written by Torsten Seemann
[05:03:10] Obtained from https://github.com/tseemann/snippy
[05:03:10] Detected operating system: linux
[05:03:10] Enabling bundled linux tools.
[05:03:10] Found bwa - /usr/local/bin/bwa
[05:03:10] Found bcftools - /usr/local/bin/bcftools
[05:03:10] Found samtools - /usr/local/bin/samtools
[05:03:10] Found java - /usr/local/bin/java
[05:03:10] Found snpEff - /usr/local/bin/snpEff
[05:03:10] Found samclip - /usr/local/bin/samclip
[05:03:10] Found seqtk - /usr/local/bin/seqtk
[05:03:10] Found parallel - /usr/local/bin/parallel
[05:03:10] Found freebayes - /usr/local/bin/freebayes
[05:03:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:10] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:10] Found gzip - /bin/gzip
[05:03:10] Found vt - /usr/local/bin/vt
[05:03:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:03:53] This is snippy 4.6.0Show full stderr[05:03:53] This is snippy 4.6.0
[05:03:53] Written by Torsten Seemann
[05:03:53] Obtained from https://github.com/tseemann/snippy
[05:03:53] Detected operating system: linux
[05:03:53] Enabling bundled linux tools.
[05:03:53] Found bwa - /usr/local/bin/bwa
[05:03:53] Found bcftools - /usr/local/bin/bcftools
[05:03:53] Found samtools - /usr/local/bin/samtools
[05:03:53] Found java - /usr/local/bin/java
[05:03:53] Found snpEff - /usr/local/bin/snpEff
[05:03:53] Found samclip - /usr/local/bin/samclip
[05:03:53] Found seqtk - /usr/local/bin/seqtk
[05:03:53] Found parallel - /usr/local/bin/parallel
[05:03:53] Found freebayes - /usr/local/bin/freebayes
[05:03:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:53] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:53] Found gzip - /bin/gzip
[05:03:53] Found vt - /usr/local/bin/vt
[05:03:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:04:59] This is snippy 4.6.0Show full stderr[05:04:59] This is snippy 4.6.0
[05:04:59] Written by Torsten Seemann
[05:04:59] Obtained from https://github.com/tseemann/snippy
[05:04:59] Detected operating system: linux
[05:04:59] Enabling bundled linux tools.
[05:04:59] Found bwa - /usr/local/bin/bwa
[05:04:59] Found bcftools - /usr/local/bin/bcftools
[05:04:59] Found samtools - /usr/local/bin/samtools
[05:04:59] Found java - /usr/local/bin/java
[05:04:59] Found snpEff - /usr/local/bin/snpEff
[05:04:59] Found samclip - /usr/local/bin/samclip
[05:04:59] Found seqtk - /usr/local/bin/seqtk
[05:04:59] Found parallel - /usr/local/bin/parallel
[05:04:59] Found freebayes - /usr/local/bin/freebayes
[05:04:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:59] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:59] Found gzip - /bin/gzip
[05:04:59] Found vt - /usr/local/bin/vt
[05:04:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:59:12] This is snippy 4.6.0Show full stderr[04:59:12] This is snippy 4.6.0
[04:59:12] Written by Torsten Seemann
[04:59:12] Obtained from https://github.com/tseemann/snippy
[04:59:12] Detected operating system: linux
[04:59:12] Enabling bundled linux tools.
[04:59:12] Found bwa - /usr/local/bin/bwa
[04:59:12] Found bcftools - /usr/local/bin/bcftools
[04:59:12] Found samtools - /usr/local/bin/samtools
[04:59:12] Found java - /usr/local/bin/java
[04:59:12] Found snpEff - /usr/local/bin/snpEff
[04:59:12] Found samclip - /usr/local/bin/samclip
[04:59:12] Found seqtk - /usr/local/bin/seqtk
[04:59:12] Found parallel - /usr/local/bin/parallel
[04:59:12] Found freebayes - /usr/local/bin/freebayes
[04:59:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:12] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:12] Found gzip - /bin/gzip
[04:59:12] Found vt - /usr/local/bin/vt
[04:59:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:59:19] This is snippy 4.6.0Show full stderr[04:59:19] This is snippy 4.6.0
[04:59:19] Written by Torsten Seemann
[04:59:19] Obtained from https://github.com/tseemann/snippy
[04:59:19] Detected operating system: linux
[04:59:19] Enabling bundled linux tools.
[04:59:19] Found bwa - /usr/local/bin/bwa
[04:59:19] Found bcftools - /usr/local/bin/bcftools
[04:59:19] Found samtools - /usr/local/bin/samtools
[04:59:19] Found java - /usr/local/bin/java
[04:59:19] Found snpEff - /usr/local/bin/snpEff
[04:59:19] Found samclip - /usr/local/bin/samclip
[04:59:19] Found seqtk - /usr/local/bin/seqtk
[04:59:19] Found parallel - /usr/local/bin/parallel
[04:59:19] Found freebayes - /usr/local/bin/freebayes
[04:59:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:19] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:19] Found gzip - /bin/gzip
[04:59:19] Found vt - /usr/local/bin/vt
[04:59:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:59:51] This is snippy 4.6.0Show full stderr[04:59:51] This is snippy 4.6.0
[04:59:51] Written by Torsten Seemann
[04:59:51] Obtained from https://github.com/tseemann/snippy
[04:59:51] Detected operating system: linux
[04:59:51] Enabling bundled linux tools.
[04:59:51] Found bwa - /usr/local/bin/bwa
[04:59:51] Found bcftools - /usr/local/bin/bcftools
[04:59:51] Found samtools - /usr/local/bin/samtools
[04:59:51] Found java - /usr/local/bin/java
[04:59:51] Found snpEff - /usr/local/bin/snpEff
[04:59:51] Found samclip - /usr/local/bin/samclip
[04:59:51] Found seqtk - /usr/local/bin/seqtk
[04:59:51] Found parallel - /usr/local/bin/parallel
[04:59:51] Found freebayes - /usr/local/bin/freebayes
[04:59:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:59:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:59:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:59:51] Found vcfuniq - /usr/local/bin/vcfuniq
[04:59:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:59:51] Found gzip - /bin/gzip
[04:59:51] Found vt - /usr/local/bin/vt
[04:59:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:59:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:59:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:59:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:59:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:59:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:59:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:59:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:03] This is snippy 4.6.0Show full stderr[05:00:03] This is snippy 4.6.0
[05:00:03] Written by Torsten Seemann
[05:00:03] Obtained from https://github.com/tseemann/snippy
[05:00:03] Detected operating system: linux
[05:00:03] Enabling bundled linux tools.
[05:00:03] Found bwa - /usr/local/bin/bwa
[05:00:03] Found bcftools - /usr/local/bin/bcftools
[05:00:03] Found samtools - /usr/local/bin/samtools
[05:00:03] Found java - /usr/local/bin/java
[05:00:03] Found snpEff - /usr/local/bin/snpEff
[05:00:03] Found samclip - /usr/local/bin/samclip
[05:00:03] Found seqtk - /usr/local/bin/seqtk
[05:00:03] Found parallel - /usr/local/bin/parallel
[05:00:03] Found freebayes - /usr/local/bin/freebayes
[05:00:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:03] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:03] Found gzip - /bin/gzip
[05:00:03] Found vt - /usr/local/bin/vt
[05:00:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:34] This is snippy 4.6.0Show full stderr[05:00:34] This is snippy 4.6.0
[05:00:34] Written by Torsten Seemann
[05:00:34] Obtained from https://github.com/tseemann/snippy
[05:00:34] Detected operating system: linux
[05:00:34] Enabling bundled linux tools.
[05:00:34] Found bwa - /usr/local/bin/bwa
[05:00:34] Found bcftools - /usr/local/bin/bcftools
[05:00:34] Found samtools - /usr/local/bin/samtools
[05:00:34] Found java - /usr/local/bin/java
[05:00:34] Found snpEff - /usr/local/bin/snpEff
[05:00:34] Found samclip - /usr/local/bin/samclip
[05:00:34] Found seqtk - /usr/local/bin/seqtk
[05:00:34] Found parallel - /usr/local/bin/parallel
[05:00:34] Found freebayes - /usr/local/bin/freebayes
[05:00:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:34] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:34] Found gzip - /bin/gzip
[05:00:34] Found vt - /usr/local/bin/vt
[05:00:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:51] This is snippy 4.6.0Show full stderr[05:00:51] This is snippy 4.6.0
[05:00:51] Written by Torsten Seemann
[05:00:51] Obtained from https://github.com/tseemann/snippy
[05:00:51] Detected operating system: linux
[05:00:51] Enabling bundled linux tools.
[05:00:51] Found bwa - /usr/local/bin/bwa
[05:00:51] Found bcftools - /usr/local/bin/bcftools
[05:00:51] Found samtools - /usr/local/bin/samtools
[05:00:51] Found java - /usr/local/bin/java
[05:00:51] Found snpEff - /usr/local/bin/snpEff
[05:00:51] Found samclip - /usr/local/bin/samclip
[05:00:51] Found seqtk - /usr/local/bin/seqtk
[05:00:51] Found parallel - /usr/local/bin/parallel
[05:00:51] Found freebayes - /usr/local/bin/freebayes
[05:00:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:51] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:51] Found gzip - /bin/gzip
[05:00:52] Found vt - /usr/local/bin/vt
[05:00:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:12] This is snippy 4.6.0Show full stderr[05:01:12] This is snippy 4.6.0
[05:01:12] Written by Torsten Seemann
[05:01:12] Obtained from https://github.com/tseemann/snippy
[05:01:12] Detected operating system: linux
[05:01:12] Enabling bundled linux tools.
[05:01:12] Found bwa - /usr/local/bin/bwa
[05:01:12] Found bcftools - /usr/local/bin/bcftools
[05:01:12] Found samtools - /usr/local/bin/samtools
[05:01:12] Found java - /usr/local/bin/java
[05:01:12] Found snpEff - /usr/local/bin/snpEff
[05:01:12] Found samclip - /usr/local/bin/samclip
[05:01:12] Found seqtk - /usr/local/bin/seqtk
[05:01:12] Found parallel - /usr/local/bin/parallel
[05:01:12] Found freebayes - /usr/local/bin/freebayes
[05:01:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:12] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:12] Found gzip - /bin/gzip
[05:01:12] Found vt - /usr/local/bin/vt
[05:01:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:40] This is snippy 4.6.0Show full stderr[05:01:40] This is snippy 4.6.0
[05:01:40] Written by Torsten Seemann
[05:01:40] Obtained from https://github.com/tseemann/snippy
[05:01:40] Detected operating system: linux
[05:01:40] Enabling bundled linux tools.
[05:01:40] Found bwa - /usr/local/bin/bwa
[05:01:40] Found bcftools - /usr/local/bin/bcftools
[05:01:40] Found samtools - /usr/local/bin/samtools
[05:01:40] Found java - /usr/local/bin/java
[05:01:40] Found snpEff - /usr/local/bin/snpEff
[05:01:40] Found samclip - /usr/local/bin/samclip
[05:01:40] Found seqtk - /usr/local/bin/seqtk
[05:01:40] Found parallel - /usr/local/bin/parallel
[05:01:40] Found freebayes - /usr/local/bin/freebayes
[05:01:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:40] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:40] Found gzip - /bin/gzip
[05:01:40] Found vt - /usr/local/bin/vt
[05:01:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:02:40] This is snippy 4.6.0Show full stderr[05:02:40] This is snippy 4.6.0
[05:02:40] Written by Torsten Seemann
[05:02:40] Obtained from https://github.com/tseemann/snippy
[05:02:40] Detected operating system: linux
[05:02:40] Enabling bundled linux tools.
[05:02:40] Found bwa - /usr/local/bin/bwa
[05:02:40] Found bcftools - /usr/local/bin/bcftools
[05:02:40] Found samtools - /usr/local/bin/samtools
[05:02:40] Found java - /usr/local/bin/java
[05:02:40] Found snpEff - /usr/local/bin/snpEff
[05:02:40] Found samclip - /usr/local/bin/samclip
[05:02:40] Found seqtk - /usr/local/bin/seqtk
[05:02:40] Found parallel - /usr/local/bin/parallel
[05:02:40] Found freebayes - /usr/local/bin/freebayes
[05:02:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:40] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:41] Found gzip - /bin/gzip
[05:02:41] Found vt - /usr/local/bin/vt
[05:02:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:02:41] This is snippy 4.6.0Show full stderr[05:02:41] This is snippy 4.6.0
[05:02:41] Written by Torsten Seemann
[05:02:41] Obtained from https://github.com/tseemann/snippy
[05:02:41] Detected operating system: linux
[05:02:41] Enabling bundled linux tools.
[05:02:41] Found bwa - /usr/local/bin/bwa
[05:02:41] Found bcftools - /usr/local/bin/bcftools
[05:02:41] Found samtools - /usr/local/bin/samtools
[05:02:41] Found java - /usr/local/bin/java
[05:02:41] Found snpEff - /usr/local/bin/snpEff
[05:02:41] Found samclip - /usr/local/bin/samclip
[05:02:41] Found seqtk - /usr/local/bin/seqtk
[05:02:41] Found parallel - /usr/local/bin/parallel
[05:02:41] Found freebayes - /usr/local/bin/freebayes
[05:02:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:41] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:41] Found gzip - /bin/gzip
[05:02:41] Found vt - /usr/local/bin/vt
[05:02:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:03:20] This is snippy 4.6.0Show full stderr[05:03:20] This is snippy 4.6.0
[05:03:20] Written by Torsten Seemann
[05:03:20] Obtained from https://github.com/tseemann/snippy
[05:03:20] Detected operating system: linux
[05:03:20] Enabling bundled linux tools.
[05:03:20] Found bwa - /usr/local/bin/bwa
[05:03:20] Found bcftools - /usr/local/bin/bcftools
[05:03:20] Found samtools - /usr/local/bin/samtools
[05:03:20] Found java - /usr/local/bin/java
[05:03:20] Found snpEff - /usr/local/bin/snpEff
[05:03:20] Found samclip - /usr/local/bin/samclip
[05:03:20] Found seqtk - /usr/local/bin/seqtk
[05:03:20] Found parallel - /usr/local/bin/parallel
[05:03:20] Found freebayes - /usr/local/bin/freebayes
[05:03:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:20] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:20] Found gzip - /bin/gzip
[05:03:20] Found vt - /usr/local/bin/vt
[05:03:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:03:35] This is snippy 4.6.0Show full stderr[05:03:35] This is snippy 4.6.0
[05:03:35] Written by Torsten Seemann
[05:03:35] Obtained from https://github.com/tseemann/snippy
[05:03:35] Detected operating system: linux
[05:03:35] Enabling bundled linux tools.
[05:03:35] Found bwa - /usr/local/bin/bwa
[05:03:35] Found bcftools - /usr/local/bin/bcftools
[05:03:35] Found samtools - /usr/local/bin/samtools
[05:03:35] Found java - /usr/local/bin/java
[05:03:35] Found snpEff - /usr/local/bin/snpEff
[05:03:35] Found samclip - /usr/local/bin/samclip
[05:03:35] Found seqtk - /usr/local/bin/seqtk
[05:03:35] Found parallel - /usr/local/bin/parallel
[05:03:35] Found freebayes - /usr/local/bin/freebayes
[05:03:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:35] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:35] Found gzip - /bin/gzip
[05:03:35] Found vt - /usr/local/bin/vt
[05:03:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:03:38] This is snippy 4.6.0Show full stderr[05:03:38] This is snippy 4.6.0
[05:03:38] Written by Torsten Seemann
[05:03:38] Obtained from https://github.com/tseemann/snippy
[05:03:38] Detected operating system: linux
[05:03:38] Enabling bundled linux tools.
[05:03:38] Found bwa - /usr/local/bin/bwa
[05:03:38] Found bcftools - /usr/local/bin/bcftools
[05:03:38] Found samtools - /usr/local/bin/samtools
[05:03:38] Found java - /usr/local/bin/java
[05:03:38] Found snpEff - /usr/local/bin/snpEff
[05:03:38] Found samclip - /usr/local/bin/samclip
[05:03:38] Found seqtk - /usr/local/bin/seqtk
[05:03:38] Found parallel - /usr/local/bin/parallel
[05:03:38] Found freebayes - /usr/local/bin/freebayes
[05:03:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:38] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:38] Found gzip - /bin/gzip
[05:03:38] Found vt - /usr/local/bin/vt
[05:03:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:04:11] This is snippy 4.6.0Show full stderr[05:04:11] This is snippy 4.6.0
[05:04:11] Written by Torsten Seemann
[05:04:11] Obtained from https://github.com/tseemann/snippy
[05:04:11] Detected operating system: linux
[05:04:11] Enabling bundled linux tools.
[05:04:11] Found bwa - /usr/local/bin/bwa
[05:04:11] Found bcftools - /usr/local/bin/bcftools
[05:04:11] Found samtools - /usr/local/bin/samtools
[05:04:11] Found java - /usr/local/bin/java
[05:04:11] Found snpEff - /usr/local/bin/snpEff
[05:04:11] Found samclip - /usr/local/bin/samclip
[05:04:11] Found seqtk - /usr/local/bin/seqtk
[05:04:11] Found parallel - /usr/local/bin/parallel
[05:04:11] Found freebayes - /usr/local/bin/freebayes
[05:04:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:11] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:11] Found gzip - /bin/gzip
[05:04:11] Found vt - /usr/local/bin/vt
[05:04:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:05:30] This is snippy 4.6.0Show full stderr[05:05:30] This is snippy 4.6.0
[05:05:30] Written by Torsten Seemann
[05:05:30] Obtained from https://github.com/tseemann/snippy
[05:05:30] Detected operating system: linux
[05:05:30] Enabling bundled linux tools.
[05:05:30] Found bwa - /usr/local/bin/bwa
[05:05:30] Found bcftools - /usr/local/bin/bcftools
[05:05:30] Found samtools - /usr/local/bin/samtools
[05:05:30] Found java - /usr/local/bin/java
[05:05:30] Found snpEff - /usr/local/bin/snpEff
[05:05:30] Found samclip - /usr/local/bin/samclip
[05:05:30] Found seqtk - /usr/local/bin/seqtk
[05:05:30] Found parallel - /usr/local/bin/parallel
[05:05:30] Found freebayes - /usr/local/bin/freebayes
[05:05:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:30] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:30] Found gzip - /bin/gzip
[05:05:30] Found vt - /usr/local/bin/vt
[05:05:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:06:03] This is snippy 4.6.0Show full stderr[05:06:03] This is snippy 4.6.0
[05:06:03] Written by Torsten Seemann
[05:06:03] Obtained from https://github.com/tseemann/snippy
[05:06:03] Detected operating system: linux
[05:06:03] Enabling bundled linux tools.
[05:06:03] Found bwa - /usr/local/bin/bwa
[05:06:03] Found bcftools - /usr/local/bin/bcftools
[05:06:03] Found samtools - /usr/local/bin/samtools
[05:06:03] Found java - /usr/local/bin/java
[05:06:03] Found snpEff - /usr/local/bin/snpEff
[05:06:03] Found samclip - /usr/local/bin/samclip
[05:06:03] Found seqtk - /usr/local/bin/seqtk
[05:06:03] Found parallel - /usr/local/bin/parallel
[05:06:03] Found freebayes - /usr/local/bin/freebayes
[05:06:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:06:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:06:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:06:03] Found vcfuniq - /usr/local/bin/vcfuniq
[05:06:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:06:03] Found gzip - /bin/gzip
[05:06:03] Found vt - /usr/local/bin/vt
[05:06:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:06:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:06:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:06:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:06:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:06:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:06:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:06:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:07:00] This is snippy 4.6.0Show full stderr[05:07:00] This is snippy 4.6.0
[05:07:00] Written by Torsten Seemann
[05:07:00] Obtained from https://github.com/tseemann/snippy
[05:07:00] Detected operating system: linux
[05:07:00] Enabling bundled linux tools.
[05:07:00] Found bwa - /usr/local/bin/bwa
[05:07:00] Found bcftools - /usr/local/bin/bcftools
[05:07:00] Found samtools - /usr/local/bin/samtools
[05:07:00] Found java - /usr/local/bin/java
[05:07:00] Found snpEff - /usr/local/bin/snpEff
[05:07:00] Found samclip - /usr/local/bin/samclip
[05:07:00] Found seqtk - /usr/local/bin/seqtk
[05:07:00] Found parallel - /usr/local/bin/parallel
[05:07:00] Found freebayes - /usr/local/bin/freebayes
[05:07:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:00] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:00] Found gzip - /bin/gzip
[05:07:00] Found vt - /usr/local/bin/vt
[05:07:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:13] This is snippy 4.6.0Show full stderr[05:00:13] This is snippy 4.6.0
[05:00:13] Written by Torsten Seemann
[05:00:13] Obtained from https://github.com/tseemann/snippy
[05:00:13] Detected operating system: linux
[05:00:13] Enabling bundled linux tools.
[05:00:13] Found bwa - /usr/local/bin/bwa
[05:00:13] Found bcftools - /usr/local/bin/bcftools
[05:00:13] Found samtools - /usr/local/bin/samtools
[05:00:13] Found java - /usr/local/bin/java
[05:00:13] Found snpEff - /usr/local/bin/snpEff
[05:00:13] Found samclip - /usr/local/bin/samclip
[05:00:13] Found seqtk - /usr/local/bin/seqtk
[05:00:13] Found parallel - /usr/local/bin/parallel
[05:00:13] Found freebayes - /usr/local/bin/freebayes
[05:00:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:13] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:13] Found gzip - /bin/gzip
[05:00:13] Found vt - /usr/local/bin/vt
[05:00:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:23] This is snippy 4.6.0Show full stderr[05:00:23] This is snippy 4.6.0
[05:00:23] Written by Torsten Seemann
[05:00:23] Obtained from https://github.com/tseemann/snippy
[05:00:23] Detected operating system: linux
[05:00:23] Enabling bundled linux tools.
[05:00:23] Found bwa - /usr/local/bin/bwa
[05:00:23] Found bcftools - /usr/local/bin/bcftools
[05:00:23] Found samtools - /usr/local/bin/samtools
[05:00:23] Found java - /usr/local/bin/java
[05:00:23] Found snpEff - /usr/local/bin/snpEff
[05:00:23] Found samclip - /usr/local/bin/samclip
[05:00:23] Found seqtk - /usr/local/bin/seqtk
[05:00:23] Found parallel - /usr/local/bin/parallel
[05:00:23] Found freebayes - /usr/local/bin/freebayes
[05:00:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:23] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:23] Found gzip - /bin/gzip
[05:00:23] Found vt - /usr/local/bin/vt
[05:00:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:39] This is snippy 4.6.0Show full stderr[05:00:39] This is snippy 4.6.0
[05:00:39] Written by Torsten Seemann
[05:00:39] Obtained from https://github.com/tseemann/snippy
[05:00:39] Detected operating system: linux
[05:00:39] Enabling bundled linux tools.
[05:00:39] Found bwa - /usr/local/bin/bwa
[05:00:39] Found bcftools - /usr/local/bin/bcftools
[05:00:39] Found samtools - /usr/local/bin/samtools
[05:00:39] Found java - /usr/local/bin/java
[05:00:39] Found snpEff - /usr/local/bin/snpEff
[05:00:39] Found samclip - /usr/local/bin/samclip
[05:00:39] Found seqtk - /usr/local/bin/seqtk
[05:00:39] Found parallel - /usr/local/bin/parallel
[05:00:39] Found freebayes - /usr/local/bin/freebayes
[05:00:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:39] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:39] Found gzip - /bin/gzip
[05:00:39] Found vt - /usr/local/bin/vt
[05:00:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:48] This is snippy 4.6.0Show full stderr[05:00:48] This is snippy 4.6.0
[05:00:48] Written by Torsten Seemann
[05:00:48] Obtained from https://github.com/tseemann/snippy
[05:00:48] Detected operating system: linux
[05:00:48] Enabling bundled linux tools.
[05:00:48] Found bwa - /usr/local/bin/bwa
[05:00:48] Found bcftools - /usr/local/bin/bcftools
[05:00:49] Found samtools - /usr/local/bin/samtools
[05:00:49] Found java - /usr/local/bin/java
[05:00:49] Found snpEff - /usr/local/bin/snpEff
[05:00:49] Found samclip - /usr/local/bin/samclip
[05:00:49] Found seqtk - /usr/local/bin/seqtk
[05:00:49] Found parallel - /usr/local/bin/parallel
[05:00:49] Found freebayes - /usr/local/bin/freebayes
[05:00:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:49] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:49] Found gzip - /bin/gzip
[05:00:49] Found vt - /usr/local/bin/vt
[05:00:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:00:55] This is snippy 4.6.0Show full stderr[05:00:55] This is snippy 4.6.0
[05:00:55] Written by Torsten Seemann
[05:00:55] Obtained from https://github.com/tseemann/snippy
[05:00:55] Detected operating system: linux
[05:00:55] Enabling bundled linux tools.
[05:00:55] Found bwa - /usr/local/bin/bwa
[05:00:55] Found bcftools - /usr/local/bin/bcftools
[05:00:55] Found samtools - /usr/local/bin/samtools
[05:00:55] Found java - /usr/local/bin/java
[05:00:55] Found snpEff - /usr/local/bin/snpEff
[05:00:55] Found samclip - /usr/local/bin/samclip
[05:00:55] Found seqtk - /usr/local/bin/seqtk
[05:00:55] Found parallel - /usr/local/bin/parallel
[05:00:55] Found freebayes - /usr/local/bin/freebayes
[05:00:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:00:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:00:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:00:55] Found vcfuniq - /usr/local/bin/vcfuniq
[05:00:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:00:55] Found gzip - /bin/gzip
[05:00:55] Found vt - /usr/local/bin/vt
[05:00:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:00:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:00:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:00:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:00:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:00:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:00:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:00:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:22] This is snippy 4.6.0Show full stderr[05:01:22] This is snippy 4.6.0
[05:01:22] Written by Torsten Seemann
[05:01:22] Obtained from https://github.com/tseemann/snippy
[05:01:22] Detected operating system: linux
[05:01:22] Enabling bundled linux tools.
[05:01:22] Found bwa - /usr/local/bin/bwa
[05:01:22] Found bcftools - /usr/local/bin/bcftools
[05:01:22] Found samtools - /usr/local/bin/samtools
[05:01:22] Found java - /usr/local/bin/java
[05:01:22] Found snpEff - /usr/local/bin/snpEff
[05:01:22] Found samclip - /usr/local/bin/samclip
[05:01:22] Found seqtk - /usr/local/bin/seqtk
[05:01:22] Found parallel - /usr/local/bin/parallel
[05:01:22] Found freebayes - /usr/local/bin/freebayes
[05:01:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:22] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:22] Found gzip - /bin/gzip
[05:01:22] Found vt - /usr/local/bin/vt
[05:01:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:34] This is snippy 4.6.0Show full stderr[05:01:34] This is snippy 4.6.0
[05:01:34] Written by Torsten Seemann
[05:01:34] Obtained from https://github.com/tseemann/snippy
[05:01:34] Detected operating system: linux
[05:01:34] Enabling bundled linux tools.
[05:01:34] Found bwa - /usr/local/bin/bwa
[05:01:34] Found bcftools - /usr/local/bin/bcftools
[05:01:34] Found samtools - /usr/local/bin/samtools
[05:01:34] Found java - /usr/local/bin/java
[05:01:34] Found snpEff - /usr/local/bin/snpEff
[05:01:34] Found samclip - /usr/local/bin/samclip
[05:01:34] Found seqtk - /usr/local/bin/seqtk
[05:01:34] Found parallel - /usr/local/bin/parallel
[05:01:34] Found freebayes - /usr/local/bin/freebayes
[05:01:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:34] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:34] Found gzip - /bin/gzip
[05:01:34] Found vt - /usr/local/bin/vt
[05:01:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:01:47] This is snippy 4.6.0Show full stderr[05:01:47] This is snippy 4.6.0
[05:01:47] Written by Torsten Seemann
[05:01:47] Obtained from https://github.com/tseemann/snippy
[05:01:47] Detected operating system: linux
[05:01:47] Enabling bundled linux tools.
[05:01:47] Found bwa - /usr/local/bin/bwa
[05:01:47] Found bcftools - /usr/local/bin/bcftools
[05:01:47] Found samtools - /usr/local/bin/samtools
[05:01:47] Found java - /usr/local/bin/java
[05:01:47] Found snpEff - /usr/local/bin/snpEff
[05:01:47] Found samclip - /usr/local/bin/samclip
[05:01:47] Found seqtk - /usr/local/bin/seqtk
[05:01:47] Found parallel - /usr/local/bin/parallel
[05:01:47] Found freebayes - /usr/local/bin/freebayes
[05:01:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:47] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:47] Found gzip - /bin/gzip
[05:01:47] Found vt - /usr/local/bin/vt
[05:01:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:02:24] This is snippy 4.6.0Show full stderr[05:02:24] This is snippy 4.6.0
[05:02:24] Written by Torsten Seemann
[05:02:24] Obtained from https://github.com/tseemann/snippy
[05:02:24] Detected operating system: linux
[05:02:24] Enabling bundled linux tools.
[05:02:24] Found bwa - /usr/local/bin/bwa
[05:02:24] Found bcftools - /usr/local/bin/bcftools
[05:02:24] Found samtools - /usr/local/bin/samtools
[05:02:24] Found java - /usr/local/bin/java
[05:02:24] Found snpEff - /usr/local/bin/snpEff
[05:02:24] Found samclip - /usr/local/bin/samclip
[05:02:24] Found seqtk - /usr/local/bin/seqtk
[05:02:24] Found parallel - /usr/local/bin/parallel
[05:02:24] Found freebayes - /usr/local/bin/freebayes
[05:02:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:24] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:24] Found gzip - /bin/gzip
[05:02:24] Found vt - /usr/local/bin/vt
[05:02:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:02:35] This is snippy 4.6.0Show full stderr[05:02:35] This is snippy 4.6.0
[05:02:35] Written by Torsten Seemann
[05:02:35] Obtained from https://github.com/tseemann/snippy
[05:02:35] Detected operating system: linux
[05:02:35] Enabling bundled linux tools.
[05:02:35] Found bwa - /usr/local/bin/bwa
[05:02:35] Found bcftools - /usr/local/bin/bcftools
[05:02:35] Found samtools - /usr/local/bin/samtools
[05:02:35] Found java - /usr/local/bin/java
[05:02:35] Found snpEff - /usr/local/bin/snpEff
[05:02:35] Found samclip - /usr/local/bin/samclip
[05:02:35] Found seqtk - /usr/local/bin/seqtk
[05:02:35] Found parallel - /usr/local/bin/parallel
[05:02:35] Found freebayes - /usr/local/bin/freebayes
[05:02:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:35] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:35] Found gzip - /bin/gzip
[05:02:35] Found vt - /usr/local/bin/vt
[05:02:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:02:26] This is snippy 4.6.0Show full stderr[05:02:26] This is snippy 4.6.0
[05:02:26] Written by Torsten Seemann
[05:02:26] Obtained from https://github.com/tseemann/snippy
[05:02:26] Detected operating system: linux
[05:02:26] Enabling bundled linux tools.
[05:02:26] Found bwa - /usr/local/bin/bwa
[05:02:26] Found bcftools - /usr/local/bin/bcftools
[05:02:26] Found samtools - /usr/local/bin/samtools
[05:02:26] Found java - /usr/local/bin/java
[05:02:26] Found snpEff - /usr/local/bin/snpEff
[05:02:27] Found samclip - /usr/local/bin/samclip
[05:02:27] Found seqtk - /usr/local/bin/seqtk
[05:02:27] Found parallel - /usr/local/bin/parallel
[05:02:27] Found freebayes - /usr/local/bin/freebayes
[05:02:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:27] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:27] Found gzip - /bin/gzip
[05:02:27] Found vt - /usr/local/bin/vt
[05:02:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:02:58] This is snippy 4.6.0Show full stderr[05:02:58] This is snippy 4.6.0
[05:02:58] Written by Torsten Seemann
[05:02:58] Obtained from https://github.com/tseemann/snippy
[05:02:58] Detected operating system: linux
[05:02:58] Enabling bundled linux tools.
[05:02:58] Found bwa - /usr/local/bin/bwa
[05:02:58] Found bcftools - /usr/local/bin/bcftools
[05:02:58] Found samtools - /usr/local/bin/samtools
[05:02:58] Found java - /usr/local/bin/java
[05:02:58] Found snpEff - /usr/local/bin/snpEff
[05:02:58] Found samclip - /usr/local/bin/samclip
[05:02:58] Found seqtk - /usr/local/bin/seqtk
[05:02:58] Found parallel - /usr/local/bin/parallel
[05:02:58] Found freebayes - /usr/local/bin/freebayes
[05:02:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:58] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:58] Found gzip - /bin/gzip
[05:02:58] Found vt - /usr/local/bin/vt
[05:02:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:03:23] This is snippy 4.6.0Show full stderr[05:03:23] This is snippy 4.6.0
[05:03:23] Written by Torsten Seemann
[05:03:23] Obtained from https://github.com/tseemann/snippy
[05:03:23] Detected operating system: linux
[05:03:23] Enabling bundled linux tools.
[05:03:23] Found bwa - /usr/local/bin/bwa
[05:03:23] Found bcftools - /usr/local/bin/bcftools
[05:03:23] Found samtools - /usr/local/bin/samtools
[05:03:23] Found java - /usr/local/bin/java
[05:03:23] Found snpEff - /usr/local/bin/snpEff
[05:03:23] Found samclip - /usr/local/bin/samclip
[05:03:23] Found seqtk - /usr/local/bin/seqtk
[05:03:23] Found parallel - /usr/local/bin/parallel
[05:03:23] Found freebayes - /usr/local/bin/freebayes
[05:03:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:23] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:23] Found gzip - /bin/gzip
[05:03:23] Found vt - /usr/local/bin/vt
[05:03:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:03:26] This is snippy 4.6.0Show full stderr[05:03:26] This is snippy 4.6.0
[05:03:26] Written by Torsten Seemann
[05:03:26] Obtained from https://github.com/tseemann/snippy
[05:03:26] Detected operating system: linux
[05:03:26] Enabling bundled linux tools.
[05:03:26] Found bwa - /usr/local/bin/bwa
[05:03:26] Found bcftools - /usr/local/bin/bcftools
[05:03:26] Found samtools - /usr/local/bin/samtools
[05:03:26] Found java - /usr/local/bin/java
[05:03:26] Found snpEff - /usr/local/bin/snpEff
[05:03:26] Found samclip - /usr/local/bin/samclip
[05:03:26] Found seqtk - /usr/local/bin/seqtk
[05:03:26] Found parallel - /usr/local/bin/parallel
[05:03:26] Found freebayes - /usr/local/bin/freebayes
[05:03:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:26] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:26] Found gzip - /bin/gzip
[05:03:26] Found vt - /usr/local/bin/vt
[05:03:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:03:43] This is snippy 4.6.0Show full stderr[05:03:43] This is snippy 4.6.0
[05:03:43] Written by Torsten Seemann
[05:03:43] Obtained from https://github.com/tseemann/snippy
[05:03:43] Detected operating system: linux
[05:03:43] Enabling bundled linux tools.
[05:03:43] Found bwa - /usr/local/bin/bwa
[05:03:43] Found bcftools - /usr/local/bin/bcftools
[05:03:43] Found samtools - /usr/local/bin/samtools
[05:03:43] Found java - /usr/local/bin/java
[05:03:43] Found snpEff - /usr/local/bin/snpEff
[05:03:43] Found samclip - /usr/local/bin/samclip
[05:03:43] Found seqtk - /usr/local/bin/seqtk
[05:03:43] Found parallel - /usr/local/bin/parallel
[05:03:43] Found freebayes - /usr/local/bin/freebayes
[05:03:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:43] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:43] Found gzip - /bin/gzip
[05:03:43] Found vt - /usr/local/bin/vt
[05:03:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:04:43] This is snippy 4.6.0Show full stderr[05:04:43] This is snippy 4.6.0
[05:04:43] Written by Torsten Seemann
[05:04:43] Obtained from https://github.com/tseemann/snippy
[05:04:43] Detected operating system: linux
[05:04:43] Enabling bundled linux tools.
[05:04:43] Found bwa - /usr/local/bin/bwa
[05:04:43] Found bcftools - /usr/local/bin/bcftools
[05:04:43] Found samtools - /usr/local/bin/samtools
[05:04:43] Found java - /usr/local/bin/java
[05:04:43] Found snpEff - /usr/local/bin/snpEff
[05:04:43] Found samclip - /usr/local/bin/samclip
[05:04:43] Found seqtk - /usr/local/bin/seqtk
[05:04:43] Found parallel - /usr/local/bin/parallel
[05:04:43] Found freebayes - /usr/local/bin/freebayes
[05:04:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:43] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:43] Found gzip - /bin/gzip
[05:04:43] Found vt - /usr/local/bin/vt
[05:04:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:04:41] This is snippy 4.6.0Show full stderr[05:04:41] This is snippy 4.6.0
[05:04:41] Written by Torsten Seemann
[05:04:41] Obtained from https://github.com/tseemann/snippy
[05:04:41] Detected operating system: linux
[05:04:41] Enabling bundled linux tools.
[05:04:41] Found bwa - /usr/local/bin/bwa
[05:04:41] Found bcftools - /usr/local/bin/bcftools
[05:04:41] Found samtools - /usr/local/bin/samtools
[05:04:41] Found java - /usr/local/bin/java
[05:04:41] Found snpEff - /usr/local/bin/snpEff
[05:04:41] Found samclip - /usr/local/bin/samclip
[05:04:41] Found seqtk - /usr/local/bin/seqtk
[05:04:41] Found parallel - /usr/local/bin/parallel
[05:04:41] Found freebayes - /usr/local/bin/freebayes
[05:04:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:41] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:41] Found gzip - /bin/gzip
[05:04:41] Found vt - /usr/local/bin/vt
[05:04:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:05:57] This is snippy 4.6.0Show full stderr[05:05:57] This is snippy 4.6.0
[05:05:57] Written by Torsten Seemann
[05:05:57] Obtained from https://github.com/tseemann/snippy
[05:05:57] Detected operating system: linux
[05:05:57] Enabling bundled linux tools.
[05:05:57] Found bwa - /usr/local/bin/bwa
[05:05:57] Found bcftools - /usr/local/bin/bcftools
[05:05:57] Found samtools - /usr/local/bin/samtools
[05:05:57] Found java - /usr/local/bin/java
[05:05:57] Found snpEff - /usr/local/bin/snpEff
[05:05:57] Found samclip - /usr/local/bin/samclip
[05:05:57] Found seqtk - /usr/local/bin/seqtk
[05:05:57] Found parallel - /usr/local/bin/parallel
[05:05:57] Found freebayes - /usr/local/bin/freebayes
[05:05:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:57] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:57] Found gzip - /bin/gzip
[05:05:57] Found vt - /usr/local/bin/vt
[05:05:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:06:02] This is snippy 4.6.0Show full stderr[05:06:02] This is snippy 4.6.0
[05:06:02] Written by Torsten Seemann
[05:06:02] Obtained from https://github.com/tseemann/snippy
[05:06:02] Detected operating system: linux
[05:06:02] Enabling bundled linux tools.
[05:06:02] Found bwa - /usr/local/bin/bwa
[05:06:02] Found bcftools - /usr/local/bin/bcftools
[05:06:02] Found samtools - /usr/local/bin/samtools
[05:06:02] Found java - /usr/local/bin/java
[05:06:02] Found snpEff - /usr/local/bin/snpEff
[05:06:02] Found samclip - /usr/local/bin/samclip
[05:06:02] Found seqtk - /usr/local/bin/seqtk
[05:06:02] Found parallel - /usr/local/bin/parallel
[05:06:02] Found freebayes - /usr/local/bin/freebayes
[05:06:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:06:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:06:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:06:02] Found vcfuniq - /usr/local/bin/vcfuniq
[05:06:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:06:02] Found gzip - /bin/gzip
[05:06:02] Found vt - /usr/local/bin/vt
[05:06:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:06:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:06:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:06:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:06:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:06:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:06:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:06:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:07:42] This is snippy 4.6.0Show full stderr[05:07:42] This is snippy 4.6.0
[05:07:42] Written by Torsten Seemann
[05:07:42] Obtained from https://github.com/tseemann/snippy
[05:07:42] Detected operating system: linux
[05:07:42] Enabling bundled linux tools.
[05:07:42] Found bwa - /usr/local/bin/bwa
[05:07:42] Found bcftools - /usr/local/bin/bcftools
[05:07:42] Found samtools - /usr/local/bin/samtools
[05:07:42] Found java - /usr/local/bin/java
[05:07:42] Found snpEff - /usr/local/bin/snpEff
[05:07:42] Found samclip - /usr/local/bin/samclip
[05:07:42] Found seqtk - /usr/local/bin/seqtk
[05:07:42] Found parallel - /usr/local/bin/parallel
[05:07:42] Found freebayes - /usr/local/bin/freebayes
[05:07:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:42] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:42] Found gzip - /bin/gzip
[05:07:42] Found vt - /usr/local/bin/vt
[05:07:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:08:27] This is snippy 4.6.0Show full stderr[05:08:27] This is snippy 4.6.0
[05:08:27] Written by Torsten Seemann
[05:08:27] Obtained from https://github.com/tseemann/snippy
[05:08:27] Detected operating system: linux
[05:08:27] Enabling bundled linux tools.
[05:08:27] Found bwa - /usr/local/bin/bwa
[05:08:27] Found bcftools - /usr/local/bin/bcftools
[05:08:27] Found samtools - /usr/local/bin/samtools
[05:08:27] Found java - /usr/local/bin/java
[05:08:27] Found snpEff - /usr/local/bin/snpEff
[05:08:27] Found samclip - /usr/local/bin/samclip
[05:08:27] Found seqtk - /usr/local/bin/seqtk
[05:08:27] Found parallel - /usr/local/bin/parallel
[05:08:27] Found freebayes - /usr/local/bin/freebayes
[05:08:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:27] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:27] Found gzip - /bin/gzip
[05:08:27] Found vt - /usr/local/bin/vt
[05:08:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:07:43] This is snippy 4.6.0Show full stderr[05:07:43] This is snippy 4.6.0
[05:07:43] Written by Torsten Seemann
[05:07:43] Obtained from https://github.com/tseemann/snippy
[05:07:43] Detected operating system: linux
[05:07:43] Enabling bundled linux tools.
[05:07:43] Found bwa - /usr/local/bin/bwa
[05:07:43] Found bcftools - /usr/local/bin/bcftools
[05:07:43] Found samtools - /usr/local/bin/samtools
[05:07:43] Found java - /usr/local/bin/java
[05:07:43] Found snpEff - /usr/local/bin/snpEff
[05:07:43] Found samclip - /usr/local/bin/samclip
[05:07:43] Found seqtk - /usr/local/bin/seqtk
[05:07:43] Found parallel - /usr/local/bin/parallel
[05:07:43] Found freebayes - /usr/local/bin/freebayes
[05:07:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:43] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:43] Found gzip - /bin/gzip
[05:07:43] Found vt - /usr/local/bin/vt
[05:07:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:07:48] This is snippy 4.6.0Show full stderr[05:07:48] This is snippy 4.6.0
[05:07:48] Written by Torsten Seemann
[05:07:48] Obtained from https://github.com/tseemann/snippy
[05:07:48] Detected operating system: linux
[05:07:48] Enabling bundled linux tools.
[05:07:48] Found bwa - /usr/local/bin/bwa
[05:07:48] Found bcftools - /usr/local/bin/bcftools
[05:07:48] Found samtools - /usr/local/bin/samtools
[05:07:48] Found java - /usr/local/bin/java
[05:07:48] Found snpEff - /usr/local/bin/snpEff
[05:07:48] Found samclip - /usr/local/bin/samclip
[05:07:48] Found seqtk - /usr/local/bin/seqtk
[05:07:48] Found parallel - /usr/local/bin/parallel
[05:07:48] Found freebayes - /usr/local/bin/freebayes
[05:07:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:48] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:48] Found gzip - /bin/gzip
[05:07:48] Found vt - /usr/local/bin/vt
[05:07:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:07:54] This is snippy 4.6.0Show full stderr[05:07:54] This is snippy 4.6.0
[05:07:54] Written by Torsten Seemann
[05:07:54] Obtained from https://github.com/tseemann/snippy
[05:07:54] Detected operating system: linux
[05:07:54] Enabling bundled linux tools.
[05:07:54] Found bwa - /usr/local/bin/bwa
[05:07:54] Found bcftools - /usr/local/bin/bcftools
[05:07:54] Found samtools - /usr/local/bin/samtools
[05:07:54] Found java - /usr/local/bin/java
[05:07:54] Found snpEff - /usr/local/bin/snpEff
[05:07:54] Found samclip - /usr/local/bin/samclip
[05:07:54] Found seqtk - /usr/local/bin/seqtk
[05:07:54] Found parallel - /usr/local/bin/parallel
[05:07:54] Found freebayes - /usr/local/bin/freebayes
[05:07:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:54] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:54] Found gzip - /bin/gzip
[05:07:54] Found vt - /usr/local/bin/vt
[05:07:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:08:03] This is snippy 4.6.0Show full stderr[05:08:03] This is snippy 4.6.0
[05:08:03] Written by Torsten Seemann
[05:08:03] Obtained from https://github.com/tseemann/snippy
[05:08:03] Detected operating system: linux
[05:08:03] Enabling bundled linux tools.
[05:08:03] Found bwa - /usr/local/bin/bwa
[05:08:03] Found bcftools - /usr/local/bin/bcftools
[05:08:03] Found samtools - /usr/local/bin/samtools
[05:08:03] Found java - /usr/local/bin/java
[05:08:03] Found snpEff - /usr/local/bin/snpEff
[05:08:03] Found samclip - /usr/local/bin/samclip
[05:08:03] Found seqtk - /usr/local/bin/seqtk
[05:08:03] Found parallel - /usr/local/bin/parallel
[05:08:03] Found freebayes - /usr/local/bin/freebayes
[05:08:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:03] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:03] Found gzip - /bin/gzip
[05:08:03] Found vt - /usr/local/bin/vt
[05:08:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:08:54] This is snippy 4.6.0Show full stderr[05:08:54] This is snippy 4.6.0
[05:08:54] Written by Torsten Seemann
[05:08:54] Obtained from https://github.com/tseemann/snippy
[05:08:54] Detected operating system: linux
[05:08:54] Enabling bundled linux tools.
[05:08:54] Found bwa - /usr/local/bin/bwa
[05:08:54] Found bcftools - /usr/local/bin/bcftools
[05:08:54] Found samtools - /usr/local/bin/samtools
[05:08:54] Found java - /usr/local/bin/java
[05:08:54] Found snpEff - /usr/local/bin/snpEff
[05:08:54] Found samclip - /usr/local/bin/samclip
[05:08:54] Found seqtk - /usr/local/bin/seqtk
[05:08:54] Found parallel - /usr/local/bin/parallel
[05:08:54] Found freebayes - /usr/local/bin/freebayes
[05:08:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:54] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:54] Found gzip - /bin/gzip
[05:08:54] Found vt - /usr/local/bin/vt
[05:08:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:02:54] This is snippy 4.6.0Show full stderr[05:02:54] This is snippy 4.6.0
[05:02:54] Written by Torsten Seemann
[05:02:54] Obtained from https://github.com/tseemann/snippy
[05:02:54] Detected operating system: linux
[05:02:54] Enabling bundled linux tools.
[05:02:54] Found bwa - /usr/local/bin/bwa
[05:02:54] Found bcftools - /usr/local/bin/bcftools
[05:02:54] Found samtools - /usr/local/bin/samtools
[05:02:54] Found java - /usr/local/bin/java
[05:02:55] Found snpEff - /usr/local/bin/snpEff
[05:02:55] Found samclip - /usr/local/bin/samclip
[05:02:55] Found seqtk - /usr/local/bin/seqtk
[05:02:55] Found parallel - /usr/local/bin/parallel
[05:02:55] Found freebayes - /usr/local/bin/freebayes
[05:02:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:55] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:55] Found gzip - /bin/gzip
[05:02:55] Found vt - /usr/local/bin/vt
[05:02:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:03:17] This is snippy 4.6.0Show full stderr[05:03:17] This is snippy 4.6.0
[05:03:17] Written by Torsten Seemann
[05:03:17] Obtained from https://github.com/tseemann/snippy
[05:03:17] Detected operating system: linux
[05:03:17] Enabling bundled linux tools.
[05:03:17] Found bwa - /usr/local/bin/bwa
[05:03:17] Found bcftools - /usr/local/bin/bcftools
[05:03:17] Found samtools - /usr/local/bin/samtools
[05:03:17] Found java - /usr/local/bin/java
[05:03:17] Found snpEff - /usr/local/bin/snpEff
[05:03:17] Found samclip - /usr/local/bin/samclip
[05:03:17] Found seqtk - /usr/local/bin/seqtk
[05:03:17] Found parallel - /usr/local/bin/parallel
[05:03:17] Found freebayes - /usr/local/bin/freebayes
[05:03:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:17] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:17] Found gzip - /bin/gzip
[05:03:17] Found vt - /usr/local/bin/vt
[05:03:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:03:50] This is snippy 4.6.0Show full stderr[05:03:50] This is snippy 4.6.0
[05:03:50] Written by Torsten Seemann
[05:03:50] Obtained from https://github.com/tseemann/snippy
[05:03:50] Detected operating system: linux
[05:03:50] Enabling bundled linux tools.
[05:03:50] Found bwa - /usr/local/bin/bwa
[05:03:50] Found bcftools - /usr/local/bin/bcftools
[05:03:50] Found samtools - /usr/local/bin/samtools
[05:03:50] Found java - /usr/local/bin/java
[05:03:50] Found snpEff - /usr/local/bin/snpEff
[05:03:50] Found samclip - /usr/local/bin/samclip
[05:03:50] Found seqtk - /usr/local/bin/seqtk
[05:03:50] Found parallel - /usr/local/bin/parallel
[05:03:50] Found freebayes - /usr/local/bin/freebayes
[05:03:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:03:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:03:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:03:50] Found vcfuniq - /usr/local/bin/vcfuniq
[05:03:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:03:50] Found gzip - /bin/gzip
[05:03:50] Found vt - /usr/local/bin/vt
[05:03:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:03:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:03:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:03:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:03:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:03:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:03:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:03:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:04:10] This is snippy 4.6.0Show full stderr[05:04:10] This is snippy 4.6.0
[05:04:10] Written by Torsten Seemann
[05:04:10] Obtained from https://github.com/tseemann/snippy
[05:04:10] Detected operating system: linux
[05:04:10] Enabling bundled linux tools.
[05:04:10] Found bwa - /usr/local/bin/bwa
[05:04:10] Found bcftools - /usr/local/bin/bcftools
[05:04:10] Found samtools - /usr/local/bin/samtools
[05:04:10] Found java - /usr/local/bin/java
[05:04:10] Found snpEff - /usr/local/bin/snpEff
[05:04:10] Found samclip - /usr/local/bin/samclip
[05:04:10] Found seqtk - /usr/local/bin/seqtk
[05:04:10] Found parallel - /usr/local/bin/parallel
[05:04:10] Found freebayes - /usr/local/bin/freebayes
[05:04:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:10] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:10] Found gzip - /bin/gzip
[05:04:10] Found vt - /usr/local/bin/vt
[05:04:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:09:49] This is snippy 4.6.0Show full stderr[05:09:49] This is snippy 4.6.0
[05:09:49] Written by Torsten Seemann
[05:09:49] Obtained from https://github.com/tseemann/snippy
[05:09:49] Detected operating system: linux
[05:09:49] Enabling bundled linux tools.
[05:09:49] Found bwa - /usr/local/bin/bwa
[05:09:49] Found bcftools - /usr/local/bin/bcftools
[05:09:49] Found samtools - /usr/local/bin/samtools
[05:09:49] Found java - /usr/local/bin/java
[05:09:49] Found snpEff - /usr/local/bin/snpEff
[05:09:49] Found samclip - /usr/local/bin/samclip
[05:09:49] Found seqtk - /usr/local/bin/seqtk
[05:09:49] Found parallel - /usr/local/bin/parallel
[05:09:49] Found freebayes - /usr/local/bin/freebayes
[05:09:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:49] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:49] Found gzip - /bin/gzip
[05:09:49] Found vt - /usr/local/bin/vt
[05:09:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:03] This is snippy 4.6.0Show full stderr[05:10:03] This is snippy 4.6.0
[05:10:03] Written by Torsten Seemann
[05:10:03] Obtained from https://github.com/tseemann/snippy
[05:10:03] Detected operating system: linux
[05:10:03] Enabling bundled linux tools.
[05:10:03] Found bwa - /usr/local/bin/bwa
[05:10:03] Found bcftools - /usr/local/bin/bcftools
[05:10:03] Found samtools - /usr/local/bin/samtools
[05:10:03] Found java - /usr/local/bin/java
[05:10:03] Found snpEff - /usr/local/bin/snpEff
[05:10:03] Found samclip - /usr/local/bin/samclip
[05:10:03] Found seqtk - /usr/local/bin/seqtk
[05:10:03] Found parallel - /usr/local/bin/parallel
[05:10:03] Found freebayes - /usr/local/bin/freebayes
[05:10:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:03] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:03] Found gzip - /bin/gzip
[05:10:03] Found vt - /usr/local/bin/vt
[05:10:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:40] This is snippy 4.6.0Show full stderr[05:10:40] This is snippy 4.6.0
[05:10:40] Written by Torsten Seemann
[05:10:40] Obtained from https://github.com/tseemann/snippy
[05:10:40] Detected operating system: linux
[05:10:40] Enabling bundled linux tools.
[05:10:40] Found bwa - /usr/local/bin/bwa
[05:10:40] Found bcftools - /usr/local/bin/bcftools
[05:10:40] Found samtools - /usr/local/bin/samtools
[05:10:40] Found java - /usr/local/bin/java
[05:10:40] Found snpEff - /usr/local/bin/snpEff
[05:10:40] Found samclip - /usr/local/bin/samclip
[05:10:40] Found seqtk - /usr/local/bin/seqtk
[05:10:40] Found parallel - /usr/local/bin/parallel
[05:10:40] Found freebayes - /usr/local/bin/freebayes
[05:10:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:40] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:40] Found gzip - /bin/gzip
[05:10:40] Found vt - /usr/local/bin/vt
[05:10:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:49] This is snippy 4.6.0Show full stderr[05:10:49] This is snippy 4.6.0
[05:10:49] Written by Torsten Seemann
[05:10:49] Obtained from https://github.com/tseemann/snippy
[05:10:49] Detected operating system: linux
[05:10:49] Enabling bundled linux tools.
[05:10:49] Found bwa - /usr/local/bin/bwa
[05:10:49] Found bcftools - /usr/local/bin/bcftools
[05:10:49] Found samtools - /usr/local/bin/samtools
[05:10:49] Found java - /usr/local/bin/java
[05:10:49] Found snpEff - /usr/local/bin/snpEff
[05:10:49] Found samclip - /usr/local/bin/samclip
[05:10:49] Found seqtk - /usr/local/bin/seqtk
[05:10:49] Found parallel - /usr/local/bin/parallel
[05:10:49] Found freebayes - /usr/local/bin/freebayes
[05:10:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:49] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:49] Found gzip - /bin/gzip
[05:10:49] Found vt - /usr/local/bin/vt
[05:10:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:51] This is snippy 4.6.0Show full stderr[05:10:51] This is snippy 4.6.0
[05:10:51] Written by Torsten Seemann
[05:10:51] Obtained from https://github.com/tseemann/snippy
[05:10:51] Detected operating system: linux
[05:10:51] Enabling bundled linux tools.
[05:10:51] Found bwa - /usr/local/bin/bwa
[05:10:51] Found bcftools - /usr/local/bin/bcftools
[05:10:51] Found samtools - /usr/local/bin/samtools
[05:10:51] Found java - /usr/local/bin/java
[05:10:51] Found snpEff - /usr/local/bin/snpEff
[05:10:51] Found samclip - /usr/local/bin/samclip
[05:10:51] Found seqtk - /usr/local/bin/seqtk
[05:10:51] Found parallel - /usr/local/bin/parallel
[05:10:51] Found freebayes - /usr/local/bin/freebayes
[05:10:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:51] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:51] Found gzip - /bin/gzip
[05:10:51] Found vt - /usr/local/bin/vt
[05:10:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:05:21] This is snippy 4.6.0Show full stderr[05:05:21] This is snippy 4.6.0
[05:05:21] Written by Torsten Seemann
[05:05:21] Obtained from https://github.com/tseemann/snippy
[05:05:21] Detected operating system: linux
[05:05:21] Enabling bundled linux tools.
[05:05:21] Found bwa - /usr/local/bin/bwa
[05:05:21] Found bcftools - /usr/local/bin/bcftools
[05:05:21] Found samtools - /usr/local/bin/samtools
[05:05:21] Found java - /usr/local/bin/java
[05:05:21] Found snpEff - /usr/local/bin/snpEff
[05:05:21] Found samclip - /usr/local/bin/samclip
[05:05:21] Found seqtk - /usr/local/bin/seqtk
[05:05:21] Found parallel - /usr/local/bin/parallel
[05:05:21] Found freebayes - /usr/local/bin/freebayes
[05:05:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:21] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:21] Found gzip - /bin/gzip
[05:05:21] Found vt - /usr/local/bin/vt
[05:05:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:05:33] This is snippy 4.6.0Show full stderr[05:05:33] This is snippy 4.6.0
[05:05:33] Written by Torsten Seemann
[05:05:33] Obtained from https://github.com/tseemann/snippy
[05:05:33] Detected operating system: linux
[05:05:33] Enabling bundled linux tools.
[05:05:33] Found bwa - /usr/local/bin/bwa
[05:05:33] Found bcftools - /usr/local/bin/bcftools
[05:05:33] Found samtools - /usr/local/bin/samtools
[05:05:33] Found java - /usr/local/bin/java
[05:05:33] Found snpEff - /usr/local/bin/snpEff
[05:05:33] Found samclip - /usr/local/bin/samclip
[05:05:33] Found seqtk - /usr/local/bin/seqtk
[05:05:33] Found parallel - /usr/local/bin/parallel
[05:05:33] Found freebayes - /usr/local/bin/freebayes
[05:05:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:33] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:33] Found gzip - /bin/gzip
[05:05:33] Found vt - /usr/local/bin/vt
[05:05:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:09:42] This is snippy 4.6.0Show full stderr[05:09:42] This is snippy 4.6.0
[05:09:42] Written by Torsten Seemann
[05:09:42] Obtained from https://github.com/tseemann/snippy
[05:09:42] Detected operating system: linux
[05:09:42] Enabling bundled linux tools.
[05:09:42] Found bwa - /usr/local/bin/bwa
[05:09:42] Found bcftools - /usr/local/bin/bcftools
[05:09:42] Found samtools - /usr/local/bin/samtools
[05:09:42] Found java - /usr/local/bin/java
[05:09:42] Found snpEff - /usr/local/bin/snpEff
[05:09:42] Found samclip - /usr/local/bin/samclip
[05:09:42] Found seqtk - /usr/local/bin/seqtk
[05:09:42] Found parallel - /usr/local/bin/parallel
[05:09:42] Found freebayes - /usr/local/bin/freebayes
[05:09:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:42] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:42] Found gzip - /bin/gzip
[05:09:42] Found vt - /usr/local/bin/vt
[05:09:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:05:15] This is snippy 4.6.0Show full stderr[05:05:15] This is snippy 4.6.0
[05:05:15] Written by Torsten Seemann
[05:05:15] Obtained from https://github.com/tseemann/snippy
[05:05:15] Detected operating system: linux
[05:05:15] Enabling bundled linux tools.
[05:05:15] Found bwa - /usr/local/bin/bwa
[05:05:15] Found bcftools - /usr/local/bin/bcftools
[05:05:15] Found samtools - /usr/local/bin/samtools
[05:05:15] Found java - /usr/local/bin/java
[05:05:15] Found snpEff - /usr/local/bin/snpEff
[05:05:15] Found samclip - /usr/local/bin/samclip
[05:05:15] Found seqtk - /usr/local/bin/seqtk
[05:05:15] Found parallel - /usr/local/bin/parallel
[05:05:15] Found freebayes - /usr/local/bin/freebayes
[05:05:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:15] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:15] Found gzip - /bin/gzip
[05:05:15] Found vt - /usr/local/bin/vt
[05:05:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:05:48] This is snippy 4.6.0Show full stderr[05:05:48] This is snippy 4.6.0
[05:05:48] Written by Torsten Seemann
[05:05:48] Obtained from https://github.com/tseemann/snippy
[05:05:48] Detected operating system: linux
[05:05:48] Enabling bundled linux tools.
[05:05:48] Found bwa - /usr/local/bin/bwa
[05:05:48] Found bcftools - /usr/local/bin/bcftools
[05:05:48] Found samtools - /usr/local/bin/samtools
[05:05:48] Found java - /usr/local/bin/java
[05:05:48] Found snpEff - /usr/local/bin/snpEff
[05:05:48] Found samclip - /usr/local/bin/samclip
[05:05:48] Found seqtk - /usr/local/bin/seqtk
[05:05:48] Found parallel - /usr/local/bin/parallel
[05:05:48] Found freebayes - /usr/local/bin/freebayes
[05:05:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:05:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:05:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:05:48] Found vcfuniq - /usr/local/bin/vcfuniq
[05:05:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:05:48] Found gzip - /bin/gzip
[05:05:48] Found vt - /usr/local/bin/vt
[05:05:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:05:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:05:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:05:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:05:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:05:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:05:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:05:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:06:18] This is snippy 4.6.0Show full stderr[05:06:18] This is snippy 4.6.0
[05:06:18] Written by Torsten Seemann
[05:06:18] Obtained from https://github.com/tseemann/snippy
[05:06:18] Detected operating system: linux
[05:06:18] Enabling bundled linux tools.
[05:06:18] Found bwa - /usr/local/bin/bwa
[05:06:18] Found bcftools - /usr/local/bin/bcftools
[05:06:18] Found samtools - /usr/local/bin/samtools
[05:06:18] Found java - /usr/local/bin/java
[05:06:18] Found snpEff - /usr/local/bin/snpEff
[05:06:18] Found samclip - /usr/local/bin/samclip
[05:06:18] Found seqtk - /usr/local/bin/seqtk
[05:06:18] Found parallel - /usr/local/bin/parallel
[05:06:18] Found freebayes - /usr/local/bin/freebayes
[05:06:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:06:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:06:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:06:18] Found vcfuniq - /usr/local/bin/vcfuniq
[05:06:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:06:18] Found gzip - /bin/gzip
[05:06:18] Found vt - /usr/local/bin/vt
[05:06:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:06:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:06:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:06:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:06:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:06:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:06:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:06:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:07:15] This is snippy 4.6.0Show full stderr[05:07:15] This is snippy 4.6.0
[05:07:15] Written by Torsten Seemann
[05:07:15] Obtained from https://github.com/tseemann/snippy
[05:07:15] Detected operating system: linux
[05:07:15] Enabling bundled linux tools.
[05:07:15] Found bwa - /usr/local/bin/bwa
[05:07:15] Found bcftools - /usr/local/bin/bcftools
[05:07:15] Found samtools - /usr/local/bin/samtools
[05:07:15] Found java - /usr/local/bin/java
[05:07:15] Found snpEff - /usr/local/bin/snpEff
[05:07:15] Found samclip - /usr/local/bin/samclip
[05:07:15] Found seqtk - /usr/local/bin/seqtk
[05:07:15] Found parallel - /usr/local/bin/parallel
[05:07:15] Found freebayes - /usr/local/bin/freebayes
[05:07:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:15] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:15] Found gzip - /bin/gzip
[05:07:15] Found vt - /usr/local/bin/vt
[05:07:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:07:24] This is snippy 4.6.0Show full stderr[05:07:24] This is snippy 4.6.0
[05:07:24] Written by Torsten Seemann
[05:07:24] Obtained from https://github.com/tseemann/snippy
[05:07:24] Detected operating system: linux
[05:07:24] Enabling bundled linux tools.
[05:07:24] Found bwa - /usr/local/bin/bwa
[05:07:24] Found bcftools - /usr/local/bin/bcftools
[05:07:24] Found samtools - /usr/local/bin/samtools
[05:07:24] Found java - /usr/local/bin/java
[05:07:24] Found snpEff - /usr/local/bin/snpEff
[05:07:24] Found samclip - /usr/local/bin/samclip
[05:07:24] Found seqtk - /usr/local/bin/seqtk
[05:07:24] Found parallel - /usr/local/bin/parallel
[05:07:24] Found freebayes - /usr/local/bin/freebayes
[05:07:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:24] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:24] Found gzip - /bin/gzip
[05:07:24] Found vt - /usr/local/bin/vt
[05:07:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:07:27] This is snippy 4.6.0Show full stderr[05:07:27] This is snippy 4.6.0
[05:07:27] Written by Torsten Seemann
[05:07:27] Obtained from https://github.com/tseemann/snippy
[05:07:27] Detected operating system: linux
[05:07:27] Enabling bundled linux tools.
[05:07:27] Found bwa - /usr/local/bin/bwa
[05:07:27] Found bcftools - /usr/local/bin/bcftools
[05:07:27] Found samtools - /usr/local/bin/samtools
[05:07:27] Found java - /usr/local/bin/java
[05:07:27] Found snpEff - /usr/local/bin/snpEff
[05:07:27] Found samclip - /usr/local/bin/samclip
[05:07:27] Found seqtk - /usr/local/bin/seqtk
[05:07:27] Found parallel - /usr/local/bin/parallel
[05:07:27] Found freebayes - /usr/local/bin/freebayes
[05:07:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:27] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:27] Found gzip - /bin/gzip
[05:07:27] Found vt - /usr/local/bin/vt
[05:07:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:07:39] This is snippy 4.6.0Show full stderr[05:07:39] This is snippy 4.6.0
[05:07:39] Written by Torsten Seemann
[05:07:39] Obtained from https://github.com/tseemann/snippy
[05:07:39] Detected operating system: linux
[05:07:39] Enabling bundled linux tools.
[05:07:39] Found bwa - /usr/local/bin/bwa
[05:07:39] Found bcftools - /usr/local/bin/bcftools
[05:07:39] Found samtools - /usr/local/bin/samtools
[05:07:39] Found java - /usr/local/bin/java
[05:07:39] Found snpEff - /usr/local/bin/snpEff
[05:07:39] Found samclip - /usr/local/bin/samclip
[05:07:39] Found seqtk - /usr/local/bin/seqtk
[05:07:39] Found parallel - /usr/local/bin/parallel
[05:07:39] Found freebayes - /usr/local/bin/freebayes
[05:07:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:07:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:07:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:07:39] Found vcfuniq - /usr/local/bin/vcfuniq
[05:07:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:07:39] Found gzip - /bin/gzip
[05:07:39] Found vt - /usr/local/bin/vt
[05:07:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:07:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:07:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:07:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:07:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:07:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:07:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:07:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:09:45] This is snippy 4.6.0Show full stderr[05:09:45] This is snippy 4.6.0
[05:09:45] Written by Torsten Seemann
[05:09:45] Obtained from https://github.com/tseemann/snippy
[05:09:45] Detected operating system: linux
[05:09:45] Enabling bundled linux tools.
[05:09:45] Found bwa - /usr/local/bin/bwa
[05:09:45] Found bcftools - /usr/local/bin/bcftools
[05:09:45] Found samtools - /usr/local/bin/samtools
[05:09:45] Found java - /usr/local/bin/java
[05:09:45] Found snpEff - /usr/local/bin/snpEff
[05:09:45] Found samclip - /usr/local/bin/samclip
[05:09:45] Found seqtk - /usr/local/bin/seqtk
[05:09:45] Found parallel - /usr/local/bin/parallel
[05:09:45] Found freebayes - /usr/local/bin/freebayes
[05:09:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:45] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:45] Found gzip - /bin/gzip
[05:09:45] Found vt - /usr/local/bin/vt
[05:09:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:09:57] This is snippy 4.6.0Show full stderr[05:09:57] This is snippy 4.6.0
[05:09:57] Written by Torsten Seemann
[05:09:57] Obtained from https://github.com/tseemann/snippy
[05:09:57] Detected operating system: linux
[05:09:57] Enabling bundled linux tools.
[05:09:57] Found bwa - /usr/local/bin/bwa
[05:09:57] Found bcftools - /usr/local/bin/bcftools
[05:09:57] Found samtools - /usr/local/bin/samtools
[05:09:57] Found java - /usr/local/bin/java
[05:09:57] Found snpEff - /usr/local/bin/snpEff
[05:09:57] Found samclip - /usr/local/bin/samclip
[05:09:57] Found seqtk - /usr/local/bin/seqtk
[05:09:57] Found parallel - /usr/local/bin/parallel
[05:09:57] Found freebayes - /usr/local/bin/freebayes
[05:09:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:57] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:57] Found gzip - /bin/gzip
[05:09:57] Found vt - /usr/local/bin/vt
[05:09:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:00] This is snippy 4.6.0Show full stderr[05:10:00] This is snippy 4.6.0
[05:10:00] Written by Torsten Seemann
[05:10:00] Obtained from https://github.com/tseemann/snippy
[05:10:00] Detected operating system: linux
[05:10:00] Enabling bundled linux tools.
[05:10:00] Found bwa - /usr/local/bin/bwa
[05:10:00] Found bcftools - /usr/local/bin/bcftools
[05:10:00] Found samtools - /usr/local/bin/samtools
[05:10:00] Found java - /usr/local/bin/java
[05:10:00] Found snpEff - /usr/local/bin/snpEff
[05:10:00] Found samclip - /usr/local/bin/samclip
[05:10:00] Found seqtk - /usr/local/bin/seqtk
[05:10:00] Found parallel - /usr/local/bin/parallel
[05:10:00] Found freebayes - /usr/local/bin/freebayes
[05:10:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:00] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:00] Found gzip - /bin/gzip
[05:10:00] Found vt - /usr/local/bin/vt
[05:10:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:06] This is snippy 4.6.0Show full stderr[05:10:06] This is snippy 4.6.0
[05:10:06] Written by Torsten Seemann
[05:10:06] Obtained from https://github.com/tseemann/snippy
[05:10:06] Detected operating system: linux
[05:10:06] Enabling bundled linux tools.
[05:10:06] Found bwa - /usr/local/bin/bwa
[05:10:06] Found bcftools - /usr/local/bin/bcftools
[05:10:06] Found samtools - /usr/local/bin/samtools
[05:10:06] Found java - /usr/local/bin/java
[05:10:06] Found snpEff - /usr/local/bin/snpEff
[05:10:06] Found samclip - /usr/local/bin/samclip
[05:10:06] Found seqtk - /usr/local/bin/seqtk
[05:10:06] Found parallel - /usr/local/bin/parallel
[05:10:06] Found freebayes - /usr/local/bin/freebayes
[05:10:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:06] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:06] Found gzip - /bin/gzip
[05:10:06] Found vt - /usr/local/bin/vt
[05:10:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:12] This is snippy 4.6.0Show full stderr[05:10:12] This is snippy 4.6.0
[05:10:12] Written by Torsten Seemann
[05:10:12] Obtained from https://github.com/tseemann/snippy
[05:10:12] Detected operating system: linux
[05:10:12] Enabling bundled linux tools.
[05:10:12] Found bwa - /usr/local/bin/bwa
[05:10:12] Found bcftools - /usr/local/bin/bcftools
[05:10:12] Found samtools - /usr/local/bin/samtools
[05:10:12] Found java - /usr/local/bin/java
[05:10:12] Found snpEff - /usr/local/bin/snpEff
[05:10:12] Found samclip - /usr/local/bin/samclip
[05:10:12] Found seqtk - /usr/local/bin/seqtk
[05:10:12] Found parallel - /usr/local/bin/parallel
[05:10:12] Found freebayes - /usr/local/bin/freebayes
[05:10:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:12] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:12] Found gzip - /bin/gzip
[05:10:12] Found vt - /usr/local/bin/vt
[05:10:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:15] This is snippy 4.6.0Show full stderr[05:10:15] This is snippy 4.6.0
[05:10:15] Written by Torsten Seemann
[05:10:15] Obtained from https://github.com/tseemann/snippy
[05:10:15] Detected operating system: linux
[05:10:15] Enabling bundled linux tools.
[05:10:15] Found bwa - /usr/local/bin/bwa
[05:10:15] Found bcftools - /usr/local/bin/bcftools
[05:10:15] Found samtools - /usr/local/bin/samtools
[05:10:15] Found java - /usr/local/bin/java
[05:10:15] Found snpEff - /usr/local/bin/snpEff
[05:10:15] Found samclip - /usr/local/bin/samclip
[05:10:15] Found seqtk - /usr/local/bin/seqtk
[05:10:15] Found parallel - /usr/local/bin/parallel
[05:10:15] Found freebayes - /usr/local/bin/freebayes
[05:10:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:15] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:15] Found gzip - /bin/gzip
[05:10:15] Found vt - /usr/local/bin/vt
[05:10:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:21] This is snippy 4.6.0Show full stderr[05:10:21] This is snippy 4.6.0
[05:10:21] Written by Torsten Seemann
[05:10:21] Obtained from https://github.com/tseemann/snippy
[05:10:21] Detected operating system: linux
[05:10:21] Enabling bundled linux tools.
[05:10:21] Found bwa - /usr/local/bin/bwa
[05:10:21] Found bcftools - /usr/local/bin/bcftools
[05:10:21] Found samtools - /usr/local/bin/samtools
[05:10:21] Found java - /usr/local/bin/java
[05:10:21] Found snpEff - /usr/local/bin/snpEff
[05:10:21] Found samclip - /usr/local/bin/samclip
[05:10:21] Found seqtk - /usr/local/bin/seqtk
[05:10:21] Found parallel - /usr/local/bin/parallel
[05:10:21] Found freebayes - /usr/local/bin/freebayes
[05:10:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:21] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:21] Found gzip - /bin/gzip
[05:10:21] Found vt - /usr/local/bin/vt
[05:10:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:30] This is snippy 4.6.0Show full stderr[05:10:30] This is snippy 4.6.0
[05:10:30] Written by Torsten Seemann
[05:10:30] Obtained from https://github.com/tseemann/snippy
[05:10:30] Detected operating system: linux
[05:10:30] Enabling bundled linux tools.
[05:10:30] Found bwa - /usr/local/bin/bwa
[05:10:30] Found bcftools - /usr/local/bin/bcftools
[05:10:30] Found samtools - /usr/local/bin/samtools
[05:10:30] Found java - /usr/local/bin/java
[05:10:30] Found snpEff - /usr/local/bin/snpEff
[05:10:30] Found samclip - /usr/local/bin/samclip
[05:10:30] Found seqtk - /usr/local/bin/seqtk
[05:10:30] Found parallel - /usr/local/bin/parallel
[05:10:30] Found freebayes - /usr/local/bin/freebayes
[05:10:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:30] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:30] Found gzip - /bin/gzip
[05:10:30] Found vt - /usr/local/bin/vt
[05:10:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:36] This is snippy 4.6.0Show full stderr[05:10:36] This is snippy 4.6.0
[05:10:36] Written by Torsten Seemann
[05:10:36] Obtained from https://github.com/tseemann/snippy
[05:10:36] Detected operating system: linux
[05:10:36] Enabling bundled linux tools.
[05:10:36] Found bwa - /usr/local/bin/bwa
[05:10:36] Found bcftools - /usr/local/bin/bcftools
[05:10:36] Found samtools - /usr/local/bin/samtools
[05:10:36] Found java - /usr/local/bin/java
[05:10:36] Found snpEff - /usr/local/bin/snpEff
[05:10:36] Found samclip - /usr/local/bin/samclip
[05:10:36] Found seqtk - /usr/local/bin/seqtk
[05:10:36] Found parallel - /usr/local/bin/parallel
[05:10:36] Found freebayes - /usr/local/bin/freebayes
[05:10:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:36] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:36] Found gzip - /bin/gzip
[05:10:36] Found vt - /usr/local/bin/vt
[05:10:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:08:06] This is snippy 4.6.0Show full stderr[05:08:06] This is snippy 4.6.0
[05:08:06] Written by Torsten Seemann
[05:08:06] Obtained from https://github.com/tseemann/snippy
[05:08:06] Detected operating system: linux
[05:08:06] Enabling bundled linux tools.
[05:08:06] Found bwa - /usr/local/bin/bwa
[05:08:06] Found bcftools - /usr/local/bin/bcftools
[05:08:06] Found samtools - /usr/local/bin/samtools
[05:08:06] Found java - /usr/local/bin/java
[05:08:06] Found snpEff - /usr/local/bin/snpEff
[05:08:06] Found samclip - /usr/local/bin/samclip
[05:08:06] Found seqtk - /usr/local/bin/seqtk
[05:08:06] Found parallel - /usr/local/bin/parallel
[05:08:06] Found freebayes - /usr/local/bin/freebayes
[05:08:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:06] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:06] Found gzip - /bin/gzip
[05:08:06] Found vt - /usr/local/bin/vt
[05:08:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:08:33] This is snippy 4.6.0Show full stderr[05:08:33] This is snippy 4.6.0
[05:08:33] Written by Torsten Seemann
[05:08:33] Obtained from https://github.com/tseemann/snippy
[05:08:33] Detected operating system: linux
[05:08:33] Enabling bundled linux tools.
[05:08:33] Found bwa - /usr/local/bin/bwa
[05:08:33] Found bcftools - /usr/local/bin/bcftools
[05:08:33] Found samtools - /usr/local/bin/samtools
[05:08:33] Found java - /usr/local/bin/java
[05:08:33] Found snpEff - /usr/local/bin/snpEff
[05:08:33] Found samclip - /usr/local/bin/samclip
[05:08:33] Found seqtk - /usr/local/bin/seqtk
[05:08:33] Found parallel - /usr/local/bin/parallel
[05:08:33] Found freebayes - /usr/local/bin/freebayes
[05:08:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:33] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:33] Found gzip - /bin/gzip
[05:08:33] Found vt - /usr/local/bin/vt
[05:08:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:08:48] This is snippy 4.6.0Show full stderr[05:08:48] This is snippy 4.6.0
[05:08:48] Written by Torsten Seemann
[05:08:48] Obtained from https://github.com/tseemann/snippy
[05:08:48] Detected operating system: linux
[05:08:48] Enabling bundled linux tools.
[05:08:48] Found bwa - /usr/local/bin/bwa
[05:08:48] Found bcftools - /usr/local/bin/bcftools
[05:08:48] Found samtools - /usr/local/bin/samtools
[05:08:48] Found java - /usr/local/bin/java
[05:08:48] Found snpEff - /usr/local/bin/snpEff
[05:08:48] Found samclip - /usr/local/bin/samclip
[05:08:48] Found seqtk - /usr/local/bin/seqtk
[05:08:48] Found parallel - /usr/local/bin/parallel
[05:08:48] Found freebayes - /usr/local/bin/freebayes
[05:08:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:48] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:48] Found gzip - /bin/gzip
[05:08:48] Found vt - /usr/local/bin/vt
[05:08:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:08:55] This is snippy 4.6.0Show full stderr[05:08:55] This is snippy 4.6.0
[05:08:55] Written by Torsten Seemann
[05:08:55] Obtained from https://github.com/tseemann/snippy
[05:08:55] Detected operating system: linux
[05:08:55] Enabling bundled linux tools.
[05:08:55] Found bwa - /usr/local/bin/bwa
[05:08:55] Found bcftools - /usr/local/bin/bcftools
[05:08:55] Found samtools - /usr/local/bin/samtools
[05:08:55] Found java - /usr/local/bin/java
[05:08:55] Found snpEff - /usr/local/bin/snpEff
[05:08:55] Found samclip - /usr/local/bin/samclip
[05:08:55] Found seqtk - /usr/local/bin/seqtk
[05:08:55] Found parallel - /usr/local/bin/parallel
[05:08:55] Found freebayes - /usr/local/bin/freebayes
[05:08:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:55] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:55] Found gzip - /bin/gzip
[05:08:55] Found vt - /usr/local/bin/vt
[05:08:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:09:00] This is snippy 4.6.0Show full stderr[05:09:00] This is snippy 4.6.0
[05:09:00] Written by Torsten Seemann
[05:09:00] Obtained from https://github.com/tseemann/snippy
[05:09:00] Detected operating system: linux
[05:09:00] Enabling bundled linux tools.
[05:09:00] Found bwa - /usr/local/bin/bwa
[05:09:00] Found bcftools - /usr/local/bin/bcftools
[05:09:00] Found samtools - /usr/local/bin/samtools
[05:09:00] Found java - /usr/local/bin/java
[05:09:00] Found snpEff - /usr/local/bin/snpEff
[05:09:00] Found samclip - /usr/local/bin/samclip
[05:09:00] Found seqtk - /usr/local/bin/seqtk
[05:09:00] Found parallel - /usr/local/bin/parallel
[05:09:00] Found freebayes - /usr/local/bin/freebayes
[05:09:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:00] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:00] Found gzip - /bin/gzip
[05:09:00] Found vt - /usr/local/bin/vt
[05:09:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:09:18] This is snippy 4.6.0Show full stderr[05:09:18] This is snippy 4.6.0
[05:09:18] Written by Torsten Seemann
[05:09:18] Obtained from https://github.com/tseemann/snippy
[05:09:18] Detected operating system: linux
[05:09:18] Enabling bundled linux tools.
[05:09:18] Found bwa - /usr/local/bin/bwa
[05:09:18] Found bcftools - /usr/local/bin/bcftools
[05:09:18] Found samtools - /usr/local/bin/samtools
[05:09:18] Found java - /usr/local/bin/java
[05:09:18] Found snpEff - /usr/local/bin/snpEff
[05:09:18] Found samclip - /usr/local/bin/samclip
[05:09:18] Found seqtk - /usr/local/bin/seqtk
[05:09:18] Found parallel - /usr/local/bin/parallel
[05:09:18] Found freebayes - /usr/local/bin/freebayes
[05:09:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:18] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:18] Found gzip - /bin/gzip
[05:09:18] Found vt - /usr/local/bin/vt
[05:09:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:11:00] This is snippy 4.6.0Show full stderr[05:11:00] This is snippy 4.6.0
[05:11:00] Written by Torsten Seemann
[05:11:00] Obtained from https://github.com/tseemann/snippy
[05:11:00] Detected operating system: linux
[05:11:00] Enabling bundled linux tools.
[05:11:00] Found bwa - /usr/local/bin/bwa
[05:11:00] Found bcftools - /usr/local/bin/bcftools
[05:11:00] Found samtools - /usr/local/bin/samtools
[05:11:00] Found java - /usr/local/bin/java
[05:11:00] Found snpEff - /usr/local/bin/snpEff
[05:11:00] Found samclip - /usr/local/bin/samclip
[05:11:00] Found seqtk - /usr/local/bin/seqtk
[05:11:00] Found parallel - /usr/local/bin/parallel
[05:11:00] Found freebayes - /usr/local/bin/freebayes
[05:11:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:11:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:11:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:11:00] Found vcfuniq - /usr/local/bin/vcfuniq
[05:11:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:11:00] Found gzip - /bin/gzip
[05:11:00] Found vt - /usr/local/bin/vt
[05:11:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:11:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:11:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:11:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:11:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:11:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:11:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:11:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:11:03] This is snippy 4.6.0Show full stderr[05:11:03] This is snippy 4.6.0
[05:11:03] Written by Torsten Seemann
[05:11:03] Obtained from https://github.com/tseemann/snippy
[05:11:03] Detected operating system: linux
[05:11:03] Enabling bundled linux tools.
[05:11:03] Found bwa - /usr/local/bin/bwa
[05:11:03] Found bcftools - /usr/local/bin/bcftools
[05:11:03] Found samtools - /usr/local/bin/samtools
[05:11:03] Found java - /usr/local/bin/java
[05:11:03] Found snpEff - /usr/local/bin/snpEff
[05:11:03] Found samclip - /usr/local/bin/samclip
[05:11:04] Found seqtk - /usr/local/bin/seqtk
[05:11:04] Found parallel - /usr/local/bin/parallel
[05:11:04] Found freebayes - /usr/local/bin/freebayes
[05:11:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:11:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:11:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:11:04] Found vcfuniq - /usr/local/bin/vcfuniq
[05:11:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:11:04] Found gzip - /bin/gzip
[05:11:04] Found vt - /usr/local/bin/vt
[05:11:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:11:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:11:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:11:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:11:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:11:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:11:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:11:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:11:12] This is snippy 4.6.0Show full stderr[05:11:12] This is snippy 4.6.0
[05:11:12] Written by Torsten Seemann
[05:11:12] Obtained from https://github.com/tseemann/snippy
[05:11:12] Detected operating system: linux
[05:11:12] Enabling bundled linux tools.
[05:11:12] Found bwa - /usr/local/bin/bwa
[05:11:12] Found bcftools - /usr/local/bin/bcftools
[05:11:12] Found samtools - /usr/local/bin/samtools
[05:11:12] Found java - /usr/local/bin/java
[05:11:12] Found snpEff - /usr/local/bin/snpEff
[05:11:12] Found samclip - /usr/local/bin/samclip
[05:11:12] Found seqtk - /usr/local/bin/seqtk
[05:11:12] Found parallel - /usr/local/bin/parallel
[05:11:12] Found freebayes - /usr/local/bin/freebayes
[05:11:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:11:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:11:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:11:12] Found vcfuniq - /usr/local/bin/vcfuniq
[05:11:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:11:12] Found gzip - /bin/gzip
[05:11:12] Found vt - /usr/local/bin/vt
[05:11:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:11:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:11:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:11:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:11:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:11:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:11:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:11:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:11:16] This is snippy 4.6.0Show full stderr[05:11:16] This is snippy 4.6.0
[05:11:16] Written by Torsten Seemann
[05:11:16] Obtained from https://github.com/tseemann/snippy
[05:11:16] Detected operating system: linux
[05:11:16] Enabling bundled linux tools.
[05:11:16] Found bwa - /usr/local/bin/bwa
[05:11:16] Found bcftools - /usr/local/bin/bcftools
[05:11:16] Found samtools - /usr/local/bin/samtools
[05:11:16] Found java - /usr/local/bin/java
[05:11:16] Found snpEff - /usr/local/bin/snpEff
[05:11:16] Found samclip - /usr/local/bin/samclip
[05:11:16] Found seqtk - /usr/local/bin/seqtk
[05:11:16] Found parallel - /usr/local/bin/parallel
[05:11:16] Found freebayes - /usr/local/bin/freebayes
[05:11:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:11:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:11:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:11:16] Found vcfuniq - /usr/local/bin/vcfuniq
[05:11:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:11:16] Found gzip - /bin/gzip
[05:11:16] Found vt - /usr/local/bin/vt
[05:11:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:11:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:11:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:11:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:11:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:11:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:11:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:11:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:11:21] This is snippy 4.6.0Show full stderr[05:11:21] This is snippy 4.6.0
[05:11:21] Written by Torsten Seemann
[05:11:21] Obtained from https://github.com/tseemann/snippy
[05:11:21] Detected operating system: linux
[05:11:21] Enabling bundled linux tools.
[05:11:21] Found bwa - /usr/local/bin/bwa
[05:11:21] Found bcftools - /usr/local/bin/bcftools
[05:11:21] Found samtools - /usr/local/bin/samtools
[05:11:21] Found java - /usr/local/bin/java
[05:11:21] Found snpEff - /usr/local/bin/snpEff
[05:11:21] Found samclip - /usr/local/bin/samclip
[05:11:21] Found seqtk - /usr/local/bin/seqtk
[05:11:21] Found parallel - /usr/local/bin/parallel
[05:11:21] Found freebayes - /usr/local/bin/freebayes
[05:11:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:11:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:11:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:11:21] Found vcfuniq - /usr/local/bin/vcfuniq
[05:11:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:11:21] Found gzip - /bin/gzip
[05:11:21] Found vt - /usr/local/bin/vt
[05:11:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:11:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:11:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:11:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:11:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:11:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:11:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:11:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:11:39] This is snippy 4.6.0Show full stderr[05:11:39] This is snippy 4.6.0
[05:11:39] Written by Torsten Seemann
[05:11:39] Obtained from https://github.com/tseemann/snippy
[05:11:39] Detected operating system: linux
[05:11:39] Enabling bundled linux tools.
[05:11:39] Found bwa - /usr/local/bin/bwa
[05:11:39] Found bcftools - /usr/local/bin/bcftools
[05:11:39] Found samtools - /usr/local/bin/samtools
[05:11:39] Found java - /usr/local/bin/java
[05:11:39] Found snpEff - /usr/local/bin/snpEff
[05:11:39] Found samclip - /usr/local/bin/samclip
[05:11:39] Found seqtk - /usr/local/bin/seqtk
[05:11:39] Found parallel - /usr/local/bin/parallel
[05:11:39] Found freebayes - /usr/local/bin/freebayes
[05:11:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:11:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:11:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:11:39] Found vcfuniq - /usr/local/bin/vcfuniq
[05:11:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:11:39] Found gzip - /bin/gzip
[05:11:39] Found vt - /usr/local/bin/vt
[05:11:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:11:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:11:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:11:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:11:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:11:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:11:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:11:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:08:18] This is snippy 4.6.0Show full stderr[05:08:18] This is snippy 4.6.0
[05:08:18] Written by Torsten Seemann
[05:08:18] Obtained from https://github.com/tseemann/snippy
[05:08:18] Detected operating system: linux
[05:08:18] Enabling bundled linux tools.
[05:08:18] Found bwa - /usr/local/bin/bwa
[05:08:18] Found bcftools - /usr/local/bin/bcftools
[05:08:18] Found samtools - /usr/local/bin/samtools
[05:08:18] Found java - /usr/local/bin/java
[05:08:18] Found snpEff - /usr/local/bin/snpEff
[05:08:18] Found samclip - /usr/local/bin/samclip
[05:08:18] Found seqtk - /usr/local/bin/seqtk
[05:08:18] Found parallel - /usr/local/bin/parallel
[05:08:18] Found freebayes - /usr/local/bin/freebayes
[05:08:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:18] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:18] Found gzip - /bin/gzip
[05:08:18] Found vt - /usr/local/bin/vt
[05:08:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:08:30] This is snippy 4.6.0Show full stderr[05:08:30] This is snippy 4.6.0
[05:08:30] Written by Torsten Seemann
[05:08:30] Obtained from https://github.com/tseemann/snippy
[05:08:30] Detected operating system: linux
[05:08:30] Enabling bundled linux tools.
[05:08:30] Found bwa - /usr/local/bin/bwa
[05:08:30] Found bcftools - /usr/local/bin/bcftools
[05:08:30] Found samtools - /usr/local/bin/samtools
[05:08:30] Found java - /usr/local/bin/java
[05:08:30] Found snpEff - /usr/local/bin/snpEff
[05:08:30] Found samclip - /usr/local/bin/samclip
[05:08:30] Found seqtk - /usr/local/bin/seqtk
[05:08:30] Found parallel - /usr/local/bin/parallel
[05:08:30] Found freebayes - /usr/local/bin/freebayes
[05:08:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:30] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:30] Found gzip - /bin/gzip
[05:08:30] Found vt - /usr/local/bin/vt
[05:08:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:08:45] This is snippy 4.6.0Show full stderr[05:08:45] This is snippy 4.6.0
[05:08:45] Written by Torsten Seemann
[05:08:45] Obtained from https://github.com/tseemann/snippy
[05:08:45] Detected operating system: linux
[05:08:45] Enabling bundled linux tools.
[05:08:45] Found bwa - /usr/local/bin/bwa
[05:08:45] Found bcftools - /usr/local/bin/bcftools
[05:08:45] Found samtools - /usr/local/bin/samtools
[05:08:45] Found java - /usr/local/bin/java
[05:08:45] Found snpEff - /usr/local/bin/snpEff
[05:08:45] Found samclip - /usr/local/bin/samclip
[05:08:45] Found seqtk - /usr/local/bin/seqtk
[05:08:45] Found parallel - /usr/local/bin/parallel
[05:08:45] Found freebayes - /usr/local/bin/freebayes
[05:08:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:08:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:08:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:08:45] Found vcfuniq - /usr/local/bin/vcfuniq
[05:08:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:08:45] Found gzip - /bin/gzip
[05:08:45] Found vt - /usr/local/bin/vt
[05:08:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:08:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:08:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:08:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:08:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:08:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:08:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:08:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:09:03] This is snippy 4.6.0Show full stderr[05:09:03] This is snippy 4.6.0
[05:09:03] Written by Torsten Seemann
[05:09:03] Obtained from https://github.com/tseemann/snippy
[05:09:03] Detected operating system: linux
[05:09:03] Enabling bundled linux tools.
[05:09:03] Found bwa - /usr/local/bin/bwa
[05:09:03] Found bcftools - /usr/local/bin/bcftools
[05:09:03] Found samtools - /usr/local/bin/samtools
[05:09:03] Found java - /usr/local/bin/java
[05:09:03] Found snpEff - /usr/local/bin/snpEff
[05:09:03] Found samclip - /usr/local/bin/samclip
[05:09:03] Found seqtk - /usr/local/bin/seqtk
[05:09:03] Found parallel - /usr/local/bin/parallel
[05:09:03] Found freebayes - /usr/local/bin/freebayes
[05:09:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:03] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:03] Found gzip - /bin/gzip
[05:09:03] Found vt - /usr/local/bin/vt
[05:09:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:09:33] This is snippy 4.6.0Show full stderr[05:09:33] This is snippy 4.6.0
[05:09:33] Written by Torsten Seemann
[05:09:33] Obtained from https://github.com/tseemann/snippy
[05:09:33] Detected operating system: linux
[05:09:33] Enabling bundled linux tools.
[05:09:33] Found bwa - /usr/local/bin/bwa
[05:09:33] Found bcftools - /usr/local/bin/bcftools
[05:09:33] Found samtools - /usr/local/bin/samtools
[05:09:33] Found java - /usr/local/bin/java
[05:09:33] Found snpEff - /usr/local/bin/snpEff
[05:09:33] Found samclip - /usr/local/bin/samclip
[05:09:33] Found seqtk - /usr/local/bin/seqtk
[05:09:33] Found parallel - /usr/local/bin/parallel
[05:09:33] Found freebayes - /usr/local/bin/freebayes
[05:09:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:09:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:09:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:09:33] Found vcfuniq - /usr/local/bin/vcfuniq
[05:09:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:09:33] Found gzip - /bin/gzip
[05:09:33] Found vt - /usr/local/bin/vt
[05:09:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:09:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:09:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:09:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:09:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:09:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:09:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:09:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:10:39] This is snippy 4.6.0Show full stderr[05:10:39] This is snippy 4.6.0
[05:10:39] Written by Torsten Seemann
[05:10:39] Obtained from https://github.com/tseemann/snippy
[05:10:39] Detected operating system: linux
[05:10:39] Enabling bundled linux tools.
[05:10:39] Found bwa - /usr/local/bin/bwa
[05:10:39] Found bcftools - /usr/local/bin/bcftools
[05:10:39] Found samtools - /usr/local/bin/samtools
[05:10:39] Found java - /usr/local/bin/java
[05:10:39] Found snpEff - /usr/local/bin/snpEff
[05:10:39] Found samclip - /usr/local/bin/samclip
[05:10:39] Found seqtk - /usr/local/bin/seqtk
[05:10:39] Found parallel - /usr/local/bin/parallel
[05:10:39] Found freebayes - /usr/local/bin/freebayes
[05:10:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:10:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:10:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:10:39] Found vcfuniq - /usr/local/bin/vcfuniq
[05:10:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:10:39] Found gzip - /bin/gzip
[05:10:39] Found vt - /usr/local/bin/vt
[05:10:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:10:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:10:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:10:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:10:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:10:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:10:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:10:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [09:51:55] This is snippy 4.6.0Show full stderr[09:51:55] This is snippy 4.6.0
[09:51:55] Written by Torsten Seemann
[09:51:55] Obtained from https://github.com/tseemann/snippy
[09:51:55] Detected operating system: linux
[09:51:55] Enabling bundled linux tools.
[09:51:55] Found bwa - /usr/local/bin/bwa
[09:51:55] Found bcftools - /usr/local/bin/bcftools
[09:51:55] Found samtools - /usr/local/bin/samtools
[09:51:55] Found java - /usr/local/bin/java
[09:51:55] Found snpEff - /usr/local/bin/snpEff
[09:51:55] Found samclip - /usr/local/bin/samclip
[09:51:55] Found seqtk - /usr/local/bin/seqtk
[09:51:55] Found parallel - /usr/local/bin/parallel
[09:51:55] Found freebayes - /usr/local/bin/freebayes
[09:51:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:51:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:51:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:51:55] Found vcfuniq - /usr/local/bin/vcfuniq
[09:51:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:51:55] Found gzip - /bin/gzip
[09:51:55] Found vt - /usr/local/bin/vt
[09:51:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:51:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:51:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:51:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:51:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:51:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:51:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:51:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [09:53:48] This is snippy 4.6.0Show full stderr[09:53:48] This is snippy 4.6.0
[09:53:48] Written by Torsten Seemann
[09:53:48] Obtained from https://github.com/tseemann/snippy
[09:53:48] Detected operating system: linux
[09:53:48] Enabling bundled linux tools.
[09:53:48] Found bwa - /usr/local/bin/bwa
[09:53:48] Found bcftools - /usr/local/bin/bcftools
[09:53:48] Found samtools - /usr/local/bin/samtools
[09:53:48] Found java - /usr/local/bin/java
[09:53:48] Found snpEff - /usr/local/bin/snpEff
[09:53:48] Found samclip - /usr/local/bin/samclip
[09:53:48] Found seqtk - /usr/local/bin/seqtk
[09:53:48] Found parallel - /usr/local/bin/parallel
[09:53:48] Found freebayes - /usr/local/bin/freebayes
[09:53:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:53:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:53:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:53:48] Found vcfuniq - /usr/local/bin/vcfuniq
[09:53:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:53:48] Found gzip - /bin/gzip
[09:53:48] Found vt - /usr/local/bin/vt
[09:53:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:53:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:53:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:53:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:53:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:53:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:53:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:53:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:41:39] This is snippy 4.6.0Show full stderr[03:41:39] This is snippy 4.6.0
[03:41:39] Written by Torsten Seemann
[03:41:39] Obtained from https://github.com/tseemann/snippy
[03:41:39] Detected operating system: linux
[03:41:39] Enabling bundled linux tools.
[03:41:39] Found bwa - /usr/local/bin/bwa
[03:41:39] Found bcftools - /usr/local/bin/bcftools
[03:41:39] Found samtools - /usr/local/bin/samtools
[03:41:39] Found java - /usr/local/bin/java
[03:41:39] Found snpEff - /usr/local/bin/snpEff
[03:41:39] Found samclip - /usr/local/bin/samclip
[03:41:39] Found seqtk - /usr/local/bin/seqtk
[03:41:39] Found parallel - /usr/local/bin/parallel
[03:41:39] Found freebayes - /usr/local/bin/freebayes
[03:41:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:41:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:41:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:41:39] Found vcfuniq - /usr/local/bin/vcfuniq
[03:41:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:41:39] Found gzip - /bin/gzip
[03:41:39] Found vt - /usr/local/bin/vt
[03:41:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:41:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:41:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:41:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:41:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:41:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:41:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:41:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:41:44] This is snippy 4.6.0Show full stderr[03:41:44] This is snippy 4.6.0
[03:41:44] Written by Torsten Seemann
[03:41:44] Obtained from https://github.com/tseemann/snippy
[03:41:44] Detected operating system: linux
[03:41:44] Enabling bundled linux tools.
[03:41:44] Found bwa - /usr/local/bin/bwa
[03:41:44] Found bcftools - /usr/local/bin/bcftools
[03:41:44] Found samtools - /usr/local/bin/samtools
[03:41:44] Found java - /usr/local/bin/java
[03:41:44] Found snpEff - /usr/local/bin/snpEff
[03:41:44] Found samclip - /usr/local/bin/samclip
[03:41:44] Found seqtk - /usr/local/bin/seqtk
[03:41:44] Found parallel - /usr/local/bin/parallel
[03:41:44] Found freebayes - /usr/local/bin/freebayes
[03:41:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:41:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:41:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:41:44] Found vcfuniq - /usr/local/bin/vcfuniq
[03:41:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:41:44] Found gzip - /bin/gzip
[03:41:44] Found vt - /usr/local/bin/vt
[03:41:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:41:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:41:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:41:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:41:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:41:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:41:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:41:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:39:43] This is snippy 4.6.0Show full stderr[03:39:43] This is snippy 4.6.0
[03:39:43] Written by Torsten Seemann
[03:39:43] Obtained from https://github.com/tseemann/snippy
[03:39:43] Detected operating system: linux
[03:39:43] Enabling bundled linux tools.
[03:39:43] Found bwa - /usr/local/bin/bwa
[03:39:43] Found bcftools - /usr/local/bin/bcftools
[03:39:43] Found samtools - /usr/local/bin/samtools
[03:39:43] Found java - /usr/local/bin/java
[03:39:43] Found snpEff - /usr/local/bin/snpEff
[03:39:43] Found samclip - /usr/local/bin/samclip
[03:39:43] Found seqtk - /usr/local/bin/seqtk
[03:39:43] Found parallel - /usr/local/bin/parallel
[03:39:43] Found freebayes - /usr/local/bin/freebayes
[03:39:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:39:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:39:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:39:43] Found vcfuniq - /usr/local/bin/vcfuniq
[03:39:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:39:43] Found gzip - /bin/gzip
[03:39:43] Found vt - /usr/local/bin/vt
[03:39:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:39:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:39:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:39:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:39:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:39:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:39:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:39:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:40:16] This is snippy 4.6.0Show full stderr[03:40:16] This is snippy 4.6.0
[03:40:16] Written by Torsten Seemann
[03:40:16] Obtained from https://github.com/tseemann/snippy
[03:40:16] Detected operating system: linux
[03:40:16] Enabling bundled linux tools.
[03:40:16] Found bwa - /usr/local/bin/bwa
[03:40:16] Found bcftools - /usr/local/bin/bcftools
[03:40:16] Found samtools - /usr/local/bin/samtools
[03:40:16] Found java - /usr/local/bin/java
[03:40:16] Found snpEff - /usr/local/bin/snpEff
[03:40:16] Found samclip - /usr/local/bin/samclip
[03:40:16] Found seqtk - /usr/local/bin/seqtk
[03:40:16] Found parallel - /usr/local/bin/parallel
[03:40:16] Found freebayes - /usr/local/bin/freebayes
[03:40:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:16] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:16] Found gzip - /bin/gzip
[03:40:16] Found vt - /usr/local/bin/vt
[03:40:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:40:19] This is snippy 4.6.0Show full stderr[03:40:19] This is snippy 4.6.0
[03:40:19] Written by Torsten Seemann
[03:40:19] Obtained from https://github.com/tseemann/snippy
[03:40:19] Detected operating system: linux
[03:40:19] Enabling bundled linux tools.
[03:40:19] Found bwa - /usr/local/bin/bwa
[03:40:19] Found bcftools - /usr/local/bin/bcftools
[03:40:19] Found samtools - /usr/local/bin/samtools
[03:40:19] Found java - /usr/local/bin/java
[03:40:19] Found snpEff - /usr/local/bin/snpEff
[03:40:19] Found samclip - /usr/local/bin/samclip
[03:40:19] Found seqtk - /usr/local/bin/seqtk
[03:40:19] Found parallel - /usr/local/bin/parallel
[03:40:19] Found freebayes - /usr/local/bin/freebayes
[03:40:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:19] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:19] Found gzip - /bin/gzip
[03:40:19] Found vt - /usr/local/bin/vt
[03:40:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:40:31] This is snippy 4.6.0Show full stderr[03:40:31] This is snippy 4.6.0
[03:40:31] Written by Torsten Seemann
[03:40:31] Obtained from https://github.com/tseemann/snippy
[03:40:31] Detected operating system: linux
[03:40:31] Enabling bundled linux tools.
[03:40:31] Found bwa - /usr/local/bin/bwa
[03:40:31] Found bcftools - /usr/local/bin/bcftools
[03:40:31] Found samtools - /usr/local/bin/samtools
[03:40:31] Found java - /usr/local/bin/java
[03:40:31] Found snpEff - /usr/local/bin/snpEff
[03:40:31] Found samclip - /usr/local/bin/samclip
[03:40:31] Found seqtk - /usr/local/bin/seqtk
[03:40:31] Found parallel - /usr/local/bin/parallel
[03:40:31] Found freebayes - /usr/local/bin/freebayes
[03:40:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:31] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:31] Found gzip - /bin/gzip
[03:40:31] Found vt - /usr/local/bin/vt
[03:40:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:40:52] This is snippy 4.6.0Show full stderr[03:40:52] This is snippy 4.6.0
[03:40:52] Written by Torsten Seemann
[03:40:52] Obtained from https://github.com/tseemann/snippy
[03:40:52] Detected operating system: linux
[03:40:52] Enabling bundled linux tools.
[03:40:52] Found bwa - /usr/local/bin/bwa
[03:40:52] Found bcftools - /usr/local/bin/bcftools
[03:40:52] Found samtools - /usr/local/bin/samtools
[03:40:52] Found java - /usr/local/bin/java
[03:40:52] Found snpEff - /usr/local/bin/snpEff
[03:40:52] Found samclip - /usr/local/bin/samclip
[03:40:52] Found seqtk - /usr/local/bin/seqtk
[03:40:52] Found parallel - /usr/local/bin/parallel
[03:40:52] Found freebayes - /usr/local/bin/freebayes
[03:40:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:52] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:52] Found gzip - /bin/gzip
[03:40:52] Found vt - /usr/local/bin/vt
[03:40:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:41:30] This is snippy 4.6.0Show full stderr[03:41:30] This is snippy 4.6.0
[03:41:30] Written by Torsten Seemann
[03:41:30] Obtained from https://github.com/tseemann/snippy
[03:41:30] Detected operating system: linux
[03:41:30] Enabling bundled linux tools.
[03:41:30] Found bwa - /usr/local/bin/bwa
[03:41:30] Found bcftools - /usr/local/bin/bcftools
[03:41:30] Found samtools - /usr/local/bin/samtools
[03:41:30] Found java - /usr/local/bin/java
[03:41:30] Found snpEff - /usr/local/bin/snpEff
[03:41:30] Found samclip - /usr/local/bin/samclip
[03:41:30] Found seqtk - /usr/local/bin/seqtk
[03:41:30] Found parallel - /usr/local/bin/parallel
[03:41:30] Found freebayes - /usr/local/bin/freebayes
[03:41:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:41:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:41:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:41:30] Found vcfuniq - /usr/local/bin/vcfuniq
[03:41:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:41:30] Found gzip - /bin/gzip
[03:41:30] Found vt - /usr/local/bin/vt
[03:41:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:41:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:41:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:41:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:41:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:41:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:41:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:41:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:39:44] This is snippy 4.6.0Show full stderr[03:39:44] This is snippy 4.6.0
[03:39:44] Written by Torsten Seemann
[03:39:44] Obtained from https://github.com/tseemann/snippy
[03:39:44] Detected operating system: linux
[03:39:44] Enabling bundled linux tools.
[03:39:44] Found bwa - /usr/local/bin/bwa
[03:39:44] Found bcftools - /usr/local/bin/bcftools
[03:39:44] Found samtools - /usr/local/bin/samtools
[03:39:44] Found java - /usr/local/bin/java
[03:39:44] Found snpEff - /usr/local/bin/snpEff
[03:39:44] Found samclip - /usr/local/bin/samclip
[03:39:44] Found seqtk - /usr/local/bin/seqtk
[03:39:44] Found parallel - /usr/local/bin/parallel
[03:39:44] Found freebayes - /usr/local/bin/freebayes
[03:39:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:39:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:39:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:39:44] Found vcfuniq - /usr/local/bin/vcfuniq
[03:39:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:39:44] Found gzip - /bin/gzip
[03:39:44] Found vt - /usr/local/bin/vt
[03:39:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:39:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:39:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:39:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:39:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:39:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:39:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:39:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:39:59] This is snippy 4.6.0Show full stderr[03:39:59] This is snippy 4.6.0
[03:39:59] Written by Torsten Seemann
[03:39:59] Obtained from https://github.com/tseemann/snippy
[03:39:59] Detected operating system: linux
[03:39:59] Enabling bundled linux tools.
[03:39:59] Found bwa - /usr/local/bin/bwa
[03:39:59] Found bcftools - /usr/local/bin/bcftools
[03:39:59] Found samtools - /usr/local/bin/samtools
[03:39:59] Found java - /usr/local/bin/java
[03:39:59] Found snpEff - /usr/local/bin/snpEff
[03:39:59] Found samclip - /usr/local/bin/samclip
[03:39:59] Found seqtk - /usr/local/bin/seqtk
[03:39:59] Found parallel - /usr/local/bin/parallel
[03:39:59] Found freebayes - /usr/local/bin/freebayes
[03:39:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:39:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:39:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:39:59] Found vcfuniq - /usr/local/bin/vcfuniq
[03:39:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:39:59] Found gzip - /bin/gzip
[03:39:59] Found vt - /usr/local/bin/vt
[03:39:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:39:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:39:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:39:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:39:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:40:02] This is snippy 4.6.0Show full stderr[03:40:02] This is snippy 4.6.0
[03:40:02] Written by Torsten Seemann
[03:40:02] Obtained from https://github.com/tseemann/snippy
[03:40:02] Detected operating system: linux
[03:40:02] Enabling bundled linux tools.
[03:40:02] Found bwa - /usr/local/bin/bwa
[03:40:02] Found bcftools - /usr/local/bin/bcftools
[03:40:02] Found samtools - /usr/local/bin/samtools
[03:40:02] Found java - /usr/local/bin/java
[03:40:02] Found snpEff - /usr/local/bin/snpEff
[03:40:02] Found samclip - /usr/local/bin/samclip
[03:40:02] Found seqtk - /usr/local/bin/seqtk
[03:40:02] Found parallel - /usr/local/bin/parallel
[03:40:02] Found freebayes - /usr/local/bin/freebayes
[03:40:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:02] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:02] Found gzip - /bin/gzip
[03:40:02] Found vt - /usr/local/bin/vt
[03:40:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:40:14] This is snippy 4.6.0Show full stderr[03:40:14] This is snippy 4.6.0
[03:40:14] Written by Torsten Seemann
[03:40:14] Obtained from https://github.com/tseemann/snippy
[03:40:14] Detected operating system: linux
[03:40:14] Enabling bundled linux tools.
[03:40:14] Found bwa - /usr/local/bin/bwa
[03:40:14] Found bcftools - /usr/local/bin/bcftools
[03:40:14] Found samtools - /usr/local/bin/samtools
[03:40:14] Found java - /usr/local/bin/java
[03:40:14] Found snpEff - /usr/local/bin/snpEff
[03:40:14] Found samclip - /usr/local/bin/samclip
[03:40:14] Found seqtk - /usr/local/bin/seqtk
[03:40:14] Found parallel - /usr/local/bin/parallel
[03:40:14] Found freebayes - /usr/local/bin/freebayes
[03:40:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:14] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:14] Found gzip - /bin/gzip
[03:40:14] Found vt - /usr/local/bin/vt
[03:40:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:40:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:40:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:40:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:40:59] This is snippy 4.6.0Show full stderr[03:40:59] This is snippy 4.6.0
[03:40:59] Written by Torsten Seemann
[03:40:59] Obtained from https://github.com/tseemann/snippy
[03:40:59] Detected operating system: linux
[03:40:59] Enabling bundled linux tools.
[03:40:59] Found bwa - /usr/local/bin/bwa
[03:40:59] Found bcftools - /usr/local/bin/bcftools
[03:40:59] Found samtools - /usr/local/bin/samtools
[03:40:59] Found java - /usr/local/bin/java
[03:40:59] Found snpEff - /usr/local/bin/snpEff
[03:40:59] Found samclip - /usr/local/bin/samclip
[03:40:59] Found seqtk - /usr/local/bin/seqtk
[03:40:59] Found parallel - /usr/local/bin/parallel
[03:40:59] Found freebayes - /usr/local/bin/freebayes
[03:40:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:40:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:40:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:40:59] Found vcfuniq - /usr/local/bin/vcfuniq
[03:40:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:40:59] Found gzip - /bin/gzip
[03:40:59] Found vt - /usr/local/bin/vt
[03:40:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:40:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:40:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:40:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:40:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:41:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:41:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:41:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:42:59] This is snippy 4.6.0Show full stderr[03:42:59] This is snippy 4.6.0
[03:42:59] Written by Torsten Seemann
[03:42:59] Obtained from https://github.com/tseemann/snippy
[03:42:59] Detected operating system: linux
[03:42:59] Enabling bundled linux tools.
[03:42:59] Found bwa - /usr/local/bin/bwa
[03:42:59] Found bcftools - /usr/local/bin/bcftools
[03:42:59] Found samtools - /usr/local/bin/samtools
[03:42:59] Found java - /usr/local/bin/java
[03:42:59] Found snpEff - /usr/local/bin/snpEff
[03:42:59] Found samclip - /usr/local/bin/samclip
[03:42:59] Found seqtk - /usr/local/bin/seqtk
[03:42:59] Found parallel - /usr/local/bin/parallel
[03:42:59] Found freebayes - /usr/local/bin/freebayes
[03:42:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:59] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:59] Found gzip - /bin/gzip
[03:42:59] Found vt - /usr/local/bin/vt
[03:42:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:42:25] This is snippy 4.6.0Show full stderr[03:42:25] This is snippy 4.6.0
[03:42:25] Written by Torsten Seemann
[03:42:25] Obtained from https://github.com/tseemann/snippy
[03:42:25] Detected operating system: linux
[03:42:25] Enabling bundled linux tools.
[03:42:25] Found bwa - /usr/local/bin/bwa
[03:42:25] Found bcftools - /usr/local/bin/bcftools
[03:42:25] Found samtools - /usr/local/bin/samtools
[03:42:25] Found java - /usr/local/bin/java
[03:42:25] Found snpEff - /usr/local/bin/snpEff
[03:42:25] Found samclip - /usr/local/bin/samclip
[03:42:25] Found seqtk - /usr/local/bin/seqtk
[03:42:25] Found parallel - /usr/local/bin/parallel
[03:42:25] Found freebayes - /usr/local/bin/freebayes
[03:42:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:25] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:25] Found gzip - /bin/gzip
[03:42:25] Found vt - /usr/local/bin/vt
[03:42:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:42:32] This is snippy 4.6.0Show full stderr[03:42:32] This is snippy 4.6.0
[03:42:32] Written by Torsten Seemann
[03:42:32] Obtained from https://github.com/tseemann/snippy
[03:42:32] Detected operating system: linux
[03:42:32] Enabling bundled linux tools.
[03:42:32] Found bwa - /usr/local/bin/bwa
[03:42:32] Found bcftools - /usr/local/bin/bcftools
[03:42:32] Found samtools - /usr/local/bin/samtools
[03:42:32] Found java - /usr/local/bin/java
[03:42:32] Found snpEff - /usr/local/bin/snpEff
[03:42:32] Found samclip - /usr/local/bin/samclip
[03:42:32] Found seqtk - /usr/local/bin/seqtk
[03:42:32] Found parallel - /usr/local/bin/parallel
[03:42:32] Found freebayes - /usr/local/bin/freebayes
[03:42:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:32] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:32] Found gzip - /bin/gzip
[03:42:32] Found vt - /usr/local/bin/vt
[03:42:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:42:41] This is snippy 4.6.0Show full stderr[03:42:41] This is snippy 4.6.0
[03:42:41] Written by Torsten Seemann
[03:42:41] Obtained from https://github.com/tseemann/snippy
[03:42:41] Detected operating system: linux
[03:42:41] Enabling bundled linux tools.
[03:42:41] Found bwa - /usr/local/bin/bwa
[03:42:41] Found bcftools - /usr/local/bin/bcftools
[03:42:41] Found samtools - /usr/local/bin/samtools
[03:42:41] Found java - /usr/local/bin/java
[03:42:41] Found snpEff - /usr/local/bin/snpEff
[03:42:41] Found samclip - /usr/local/bin/samclip
[03:42:41] Found seqtk - /usr/local/bin/seqtk
[03:42:41] Found parallel - /usr/local/bin/parallel
[03:42:41] Found freebayes - /usr/local/bin/freebayes
[03:42:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:41] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:41] Found gzip - /bin/gzip
[03:42:41] Found vt - /usr/local/bin/vt
[03:42:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:13] This is snippy 4.6.0Show full stderr[03:43:13] This is snippy 4.6.0
[03:43:13] Written by Torsten Seemann
[03:43:13] Obtained from https://github.com/tseemann/snippy
[03:43:13] Detected operating system: linux
[03:43:13] Enabling bundled linux tools.
[03:43:13] Found bwa - /usr/local/bin/bwa
[03:43:13] Found bcftools - /usr/local/bin/bcftools
[03:43:13] Found samtools - /usr/local/bin/samtools
[03:43:13] Found java - /usr/local/bin/java
[03:43:13] Found snpEff - /usr/local/bin/snpEff
[03:43:13] Found samclip - /usr/local/bin/samclip
[03:43:13] Found seqtk - /usr/local/bin/seqtk
[03:43:13] Found parallel - /usr/local/bin/parallel
[03:43:13] Found freebayes - /usr/local/bin/freebayes
[03:43:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:13] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:13] Found gzip - /bin/gzip
[03:43:13] Found vt - /usr/local/bin/vt
[03:43:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:19] This is snippy 4.6.0Show full stderr[03:43:19] This is snippy 4.6.0
[03:43:19] Written by Torsten Seemann
[03:43:19] Obtained from https://github.com/tseemann/snippy
[03:43:19] Detected operating system: linux
[03:43:19] Enabling bundled linux tools.
[03:43:19] Found bwa - /usr/local/bin/bwa
[03:43:19] Found bcftools - /usr/local/bin/bcftools
[03:43:19] Found samtools - /usr/local/bin/samtools
[03:43:19] Found java - /usr/local/bin/java
[03:43:19] Found snpEff - /usr/local/bin/snpEff
[03:43:19] Found samclip - /usr/local/bin/samclip
[03:43:19] Found seqtk - /usr/local/bin/seqtk
[03:43:19] Found parallel - /usr/local/bin/parallel
[03:43:19] Found freebayes - /usr/local/bin/freebayes
[03:43:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:19] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:19] Found gzip - /bin/gzip
[03:43:19] Found vt - /usr/local/bin/vt
[03:43:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:22] This is snippy 4.6.0Show full stderr[03:43:22] This is snippy 4.6.0
[03:43:22] Written by Torsten Seemann
[03:43:22] Obtained from https://github.com/tseemann/snippy
[03:43:22] Detected operating system: linux
[03:43:22] Enabling bundled linux tools.
[03:43:22] Found bwa - /usr/local/bin/bwa
[03:43:22] Found bcftools - /usr/local/bin/bcftools
[03:43:22] Found samtools - /usr/local/bin/samtools
[03:43:22] Found java - /usr/local/bin/java
[03:43:22] Found snpEff - /usr/local/bin/snpEff
[03:43:22] Found samclip - /usr/local/bin/samclip
[03:43:22] Found seqtk - /usr/local/bin/seqtk
[03:43:22] Found parallel - /usr/local/bin/parallel
[03:43:22] Found freebayes - /usr/local/bin/freebayes
[03:43:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:22] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:22] Found gzip - /bin/gzip
[03:43:22] Found vt - /usr/local/bin/vt
[03:43:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:34] This is snippy 4.6.0Show full stderr[03:43:34] This is snippy 4.6.0
[03:43:34] Written by Torsten Seemann
[03:43:34] Obtained from https://github.com/tseemann/snippy
[03:43:34] Detected operating system: linux
[03:43:34] Enabling bundled linux tools.
[03:43:34] Found bwa - /usr/local/bin/bwa
[03:43:34] Found bcftools - /usr/local/bin/bcftools
[03:43:34] Found samtools - /usr/local/bin/samtools
[03:43:34] Found java - /usr/local/bin/java
[03:43:34] Found snpEff - /usr/local/bin/snpEff
[03:43:34] Found samclip - /usr/local/bin/samclip
[03:43:34] Found seqtk - /usr/local/bin/seqtk
[03:43:34] Found parallel - /usr/local/bin/parallel
[03:43:34] Found freebayes - /usr/local/bin/freebayes
[03:43:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:34] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:34] Found gzip - /bin/gzip
[03:43:34] Found vt - /usr/local/bin/vt
[03:43:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:44] This is snippy 4.6.0Show full stderr[03:43:44] This is snippy 4.6.0
[03:43:44] Written by Torsten Seemann
[03:43:44] Obtained from https://github.com/tseemann/snippy
[03:43:44] Detected operating system: linux
[03:43:44] Enabling bundled linux tools.
[03:43:44] Found bwa - /usr/local/bin/bwa
[03:43:44] Found bcftools - /usr/local/bin/bcftools
[03:43:44] Found samtools - /usr/local/bin/samtools
[03:43:44] Found java - /usr/local/bin/java
[03:43:44] Found snpEff - /usr/local/bin/snpEff
[03:43:44] Found samclip - /usr/local/bin/samclip
[03:43:44] Found seqtk - /usr/local/bin/seqtk
[03:43:44] Found parallel - /usr/local/bin/parallel
[03:43:44] Found freebayes - /usr/local/bin/freebayes
[03:43:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:44] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:44] Found gzip - /bin/gzip
[03:43:44] Found vt - /usr/local/bin/vt
[03:43:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:42:18] This is snippy 4.6.0Show full stderr[03:42:18] This is snippy 4.6.0
[03:42:18] Written by Torsten Seemann
[03:42:18] Obtained from https://github.com/tseemann/snippy
[03:42:18] Detected operating system: linux
[03:42:18] Enabling bundled linux tools.
[03:42:18] Found bwa - /usr/local/bin/bwa
[03:42:18] Found bcftools - /usr/local/bin/bcftools
[03:42:18] Found samtools - /usr/local/bin/samtools
[03:42:18] Found java - /usr/local/bin/java
[03:42:18] Found snpEff - /usr/local/bin/snpEff
[03:42:18] Found samclip - /usr/local/bin/samclip
[03:42:18] Found seqtk - /usr/local/bin/seqtk
[03:42:18] Found parallel - /usr/local/bin/parallel
[03:42:18] Found freebayes - /usr/local/bin/freebayes
[03:42:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:18] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:18] Found gzip - /bin/gzip
[03:42:18] Found vt - /usr/local/bin/vt
[03:42:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:42:22] This is snippy 4.6.0Show full stderr[03:42:22] This is snippy 4.6.0
[03:42:22] Written by Torsten Seemann
[03:42:22] Obtained from https://github.com/tseemann/snippy
[03:42:22] Detected operating system: linux
[03:42:22] Enabling bundled linux tools.
[03:42:22] Found bwa - /usr/local/bin/bwa
[03:42:22] Found bcftools - /usr/local/bin/bcftools
[03:42:22] Found samtools - /usr/local/bin/samtools
[03:42:22] Found java - /usr/local/bin/java
[03:42:22] Found snpEff - /usr/local/bin/snpEff
[03:42:22] Found samclip - /usr/local/bin/samclip
[03:42:22] Found seqtk - /usr/local/bin/seqtk
[03:42:22] Found parallel - /usr/local/bin/parallel
[03:42:22] Found freebayes - /usr/local/bin/freebayes
[03:42:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:22] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:22] Found gzip - /bin/gzip
[03:42:22] Found vt - /usr/local/bin/vt
[03:42:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:31] This is snippy 4.6.0Show full stderr[03:43:31] This is snippy 4.6.0
[03:43:31] Written by Torsten Seemann
[03:43:31] Obtained from https://github.com/tseemann/snippy
[03:43:31] Detected operating system: linux
[03:43:31] Enabling bundled linux tools.
[03:43:31] Found bwa - /usr/local/bin/bwa
[03:43:31] Found bcftools - /usr/local/bin/bcftools
[03:43:31] Found samtools - /usr/local/bin/samtools
[03:43:31] Found java - /usr/local/bin/java
[03:43:31] Found snpEff - /usr/local/bin/snpEff
[03:43:31] Found samclip - /usr/local/bin/samclip
[03:43:31] Found seqtk - /usr/local/bin/seqtk
[03:43:31] Found parallel - /usr/local/bin/parallel
[03:43:31] Found freebayes - /usr/local/bin/freebayes
[03:43:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:31] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:31] Found gzip - /bin/gzip
[03:43:31] Found vt - /usr/local/bin/vt
[03:43:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:40] This is snippy 4.6.0Show full stderr[03:43:40] This is snippy 4.6.0
[03:43:40] Written by Torsten Seemann
[03:43:40] Obtained from https://github.com/tseemann/snippy
[03:43:40] Detected operating system: linux
[03:43:40] Enabling bundled linux tools.
[03:43:40] Found bwa - /usr/local/bin/bwa
[03:43:40] Found bcftools - /usr/local/bin/bcftools
[03:43:40] Found samtools - /usr/local/bin/samtools
[03:43:40] Found java - /usr/local/bin/java
[03:43:40] Found snpEff - /usr/local/bin/snpEff
[03:43:40] Found samclip - /usr/local/bin/samclip
[03:43:40] Found seqtk - /usr/local/bin/seqtk
[03:43:40] Found parallel - /usr/local/bin/parallel
[03:43:40] Found freebayes - /usr/local/bin/freebayes
[03:43:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:40] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:40] Found gzip - /bin/gzip
[03:43:40] Found vt - /usr/local/bin/vt
[03:43:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:44:00] This is snippy 4.6.0Show full stderr[03:44:00] This is snippy 4.6.0
[03:44:00] Written by Torsten Seemann
[03:44:00] Obtained from https://github.com/tseemann/snippy
[03:44:00] Detected operating system: linux
[03:44:00] Enabling bundled linux tools.
[03:44:00] Found bwa - /usr/local/bin/bwa
[03:44:00] Found bcftools - /usr/local/bin/bcftools
[03:44:00] Found samtools - /usr/local/bin/samtools
[03:44:00] Found java - /usr/local/bin/java
[03:44:00] Found snpEff - /usr/local/bin/snpEff
[03:44:00] Found samclip - /usr/local/bin/samclip
[03:44:00] Found seqtk - /usr/local/bin/seqtk
[03:44:00] Found parallel - /usr/local/bin/parallel
[03:44:00] Found freebayes - /usr/local/bin/freebayes
[03:44:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:44:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:44:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:44:00] Found vcfuniq - /usr/local/bin/vcfuniq
[03:44:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:44:00] Found gzip - /bin/gzip
[03:44:00] Found vt - /usr/local/bin/vt
[03:44:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:44:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:44:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:44:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:44:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:44:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:44:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:44:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:44:04] This is snippy 4.6.0Show full stderr[03:44:04] This is snippy 4.6.0
[03:44:04] Written by Torsten Seemann
[03:44:04] Obtained from https://github.com/tseemann/snippy
[03:44:04] Detected operating system: linux
[03:44:04] Enabling bundled linux tools.
[03:44:04] Found bwa - /usr/local/bin/bwa
[03:44:04] Found bcftools - /usr/local/bin/bcftools
[03:44:04] Found samtools - /usr/local/bin/samtools
[03:44:04] Found java - /usr/local/bin/java
[03:44:04] Found snpEff - /usr/local/bin/snpEff
[03:44:04] Found samclip - /usr/local/bin/samclip
[03:44:04] Found seqtk - /usr/local/bin/seqtk
[03:44:04] Found parallel - /usr/local/bin/parallel
[03:44:04] Found freebayes - /usr/local/bin/freebayes
[03:44:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:44:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:44:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:44:04] Found vcfuniq - /usr/local/bin/vcfuniq
[03:44:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:44:04] Found gzip - /bin/gzip
[03:44:04] Found vt - /usr/local/bin/vt
[03:44:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:44:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:44:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:44:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:44:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:44:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:44:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:44:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:44:20] This is snippy 4.6.0Show full stderr[03:44:20] This is snippy 4.6.0
[03:44:20] Written by Torsten Seemann
[03:44:20] Obtained from https://github.com/tseemann/snippy
[03:44:20] Detected operating system: linux
[03:44:20] Enabling bundled linux tools.
[03:44:20] Found bwa - /usr/local/bin/bwa
[03:44:20] Found bcftools - /usr/local/bin/bcftools
[03:44:20] Found samtools - /usr/local/bin/samtools
[03:44:20] Found java - /usr/local/bin/java
[03:44:20] Found snpEff - /usr/local/bin/snpEff
[03:44:20] Found samclip - /usr/local/bin/samclip
[03:44:20] Found seqtk - /usr/local/bin/seqtk
[03:44:20] Found parallel - /usr/local/bin/parallel
[03:44:20] Found freebayes - /usr/local/bin/freebayes
[03:44:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:44:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:44:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:44:20] Found vcfuniq - /usr/local/bin/vcfuniq
[03:44:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:44:20] Found gzip - /bin/gzip
[03:44:20] Found vt - /usr/local/bin/vt
[03:44:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:44:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:44:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:44:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:44:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:44:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:44:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:44:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:42:13] This is snippy 4.6.0Show full stderr[03:42:13] This is snippy 4.6.0
[03:42:13] Written by Torsten Seemann
[03:42:13] Obtained from https://github.com/tseemann/snippy
[03:42:13] Detected operating system: linux
[03:42:13] Enabling bundled linux tools.
[03:42:13] Found bwa - /usr/local/bin/bwa
[03:42:13] Found bcftools - /usr/local/bin/bcftools
[03:42:13] Found samtools - /usr/local/bin/samtools
[03:42:13] Found java - /usr/local/bin/java
[03:42:13] Found snpEff - /usr/local/bin/snpEff
[03:42:13] Found samclip - /usr/local/bin/samclip
[03:42:13] Found seqtk - /usr/local/bin/seqtk
[03:42:13] Found parallel - /usr/local/bin/parallel
[03:42:13] Found freebayes - /usr/local/bin/freebayes
[03:42:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:13] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:13] Found gzip - /bin/gzip
[03:42:13] Found vt - /usr/local/bin/vt
[03:42:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:42:50] This is snippy 4.6.0Show full stderr[03:42:50] This is snippy 4.6.0
[03:42:50] Written by Torsten Seemann
[03:42:50] Obtained from https://github.com/tseemann/snippy
[03:42:50] Detected operating system: linux
[03:42:50] Enabling bundled linux tools.
[03:42:50] Found bwa - /usr/local/bin/bwa
[03:42:50] Found bcftools - /usr/local/bin/bcftools
[03:42:50] Found samtools - /usr/local/bin/samtools
[03:42:50] Found java - /usr/local/bin/java
[03:42:50] Found snpEff - /usr/local/bin/snpEff
[03:42:50] Found samclip - /usr/local/bin/samclip
[03:42:50] Found seqtk - /usr/local/bin/seqtk
[03:42:50] Found parallel - /usr/local/bin/parallel
[03:42:50] Found freebayes - /usr/local/bin/freebayes
[03:42:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:42:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:42:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:42:50] Found vcfuniq - /usr/local/bin/vcfuniq
[03:42:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:42:50] Found gzip - /bin/gzip
[03:42:50] Found vt - /usr/local/bin/vt
[03:42:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:42:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:42:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:42:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:42:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:42:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:42:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:42:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:14] This is snippy 4.6.0Show full stderr[03:43:14] This is snippy 4.6.0
[03:43:14] Written by Torsten Seemann
[03:43:14] Obtained from https://github.com/tseemann/snippy
[03:43:14] Detected operating system: linux
[03:43:14] Enabling bundled linux tools.
[03:43:14] Found bwa - /usr/local/bin/bwa
[03:43:14] Found bcftools - /usr/local/bin/bcftools
[03:43:14] Found samtools - /usr/local/bin/samtools
[03:43:14] Found java - /usr/local/bin/java
[03:43:14] Found snpEff - /usr/local/bin/snpEff
[03:43:14] Found samclip - /usr/local/bin/samclip
[03:43:14] Found seqtk - /usr/local/bin/seqtk
[03:43:14] Found parallel - /usr/local/bin/parallel
[03:43:14] Found freebayes - /usr/local/bin/freebayes
[03:43:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:14] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:14] Found gzip - /bin/gzip
[03:43:14] Found vt - /usr/local/bin/vt
[03:43:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:25] This is snippy 4.6.0Show full stderr[03:43:25] This is snippy 4.6.0
[03:43:25] Written by Torsten Seemann
[03:43:25] Obtained from https://github.com/tseemann/snippy
[03:43:25] Detected operating system: linux
[03:43:25] Enabling bundled linux tools.
[03:43:25] Found bwa - /usr/local/bin/bwa
[03:43:25] Found bcftools - /usr/local/bin/bcftools
[03:43:25] Found samtools - /usr/local/bin/samtools
[03:43:25] Found java - /usr/local/bin/java
[03:43:25] Found snpEff - /usr/local/bin/snpEff
[03:43:25] Found samclip - /usr/local/bin/samclip
[03:43:25] Found seqtk - /usr/local/bin/seqtk
[03:43:25] Found parallel - /usr/local/bin/parallel
[03:43:25] Found freebayes - /usr/local/bin/freebayes
[03:43:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:25] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:25] Found gzip - /bin/gzip
[03:43:25] Found vt - /usr/local/bin/vt
[03:43:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:37] This is snippy 4.6.0Show full stderr[03:43:37] This is snippy 4.6.0
[03:43:37] Written by Torsten Seemann
[03:43:37] Obtained from https://github.com/tseemann/snippy
[03:43:37] Detected operating system: linux
[03:43:37] Enabling bundled linux tools.
[03:43:37] Found bwa - /usr/local/bin/bwa
[03:43:37] Found bcftools - /usr/local/bin/bcftools
[03:43:37] Found samtools - /usr/local/bin/samtools
[03:43:37] Found java - /usr/local/bin/java
[03:43:37] Found snpEff - /usr/local/bin/snpEff
[03:43:37] Found samclip - /usr/local/bin/samclip
[03:43:37] Found seqtk - /usr/local/bin/seqtk
[03:43:37] Found parallel - /usr/local/bin/parallel
[03:43:37] Found freebayes - /usr/local/bin/freebayes
[03:43:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:37] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:37] Found gzip - /bin/gzip
[03:43:37] Found vt - /usr/local/bin/vt
[03:43:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:49] This is snippy 4.6.0Show full stderr[03:43:49] This is snippy 4.6.0
[03:43:49] Written by Torsten Seemann
[03:43:49] Obtained from https://github.com/tseemann/snippy
[03:43:49] Detected operating system: linux
[03:43:49] Enabling bundled linux tools.
[03:43:49] Found bwa - /usr/local/bin/bwa
[03:43:49] Found bcftools - /usr/local/bin/bcftools
[03:43:49] Found samtools - /usr/local/bin/samtools
[03:43:49] Found java - /usr/local/bin/java
[03:43:49] Found snpEff - /usr/local/bin/snpEff
[03:43:49] Found samclip - /usr/local/bin/samclip
[03:43:49] Found seqtk - /usr/local/bin/seqtk
[03:43:49] Found parallel - /usr/local/bin/parallel
[03:43:49] Found freebayes - /usr/local/bin/freebayes
[03:43:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:49] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:49] Found gzip - /bin/gzip
[03:43:49] Found vt - /usr/local/bin/vt
[03:43:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:52] This is snippy 4.6.0Show full stderr[03:43:52] This is snippy 4.6.0
[03:43:52] Written by Torsten Seemann
[03:43:52] Obtained from https://github.com/tseemann/snippy
[03:43:52] Detected operating system: linux
[03:43:52] Enabling bundled linux tools.
[03:43:52] Found bwa - /usr/local/bin/bwa
[03:43:52] Found bcftools - /usr/local/bin/bcftools
[03:43:52] Found samtools - /usr/local/bin/samtools
[03:43:52] Found java - /usr/local/bin/java
[03:43:52] Found snpEff - /usr/local/bin/snpEff
[03:43:52] Found samclip - /usr/local/bin/samclip
[03:43:52] Found seqtk - /usr/local/bin/seqtk
[03:43:52] Found parallel - /usr/local/bin/parallel
[03:43:52] Found freebayes - /usr/local/bin/freebayes
[03:43:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:52] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:52] Found gzip - /bin/gzip
[03:43:52] Found vt - /usr/local/bin/vt
[03:43:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:44:10] This is snippy 4.6.0Show full stderr[03:44:10] This is snippy 4.6.0
[03:44:10] Written by Torsten Seemann
[03:44:10] Obtained from https://github.com/tseemann/snippy
[03:44:10] Detected operating system: linux
[03:44:10] Enabling bundled linux tools.
[03:44:10] Found bwa - /usr/local/bin/bwa
[03:44:10] Found bcftools - /usr/local/bin/bcftools
[03:44:10] Found samtools - /usr/local/bin/samtools
[03:44:10] Found java - /usr/local/bin/java
[03:44:10] Found snpEff - /usr/local/bin/snpEff
[03:44:10] Found samclip - /usr/local/bin/samclip
[03:44:10] Found seqtk - /usr/local/bin/seqtk
[03:44:10] Found parallel - /usr/local/bin/parallel
[03:44:10] Found freebayes - /usr/local/bin/freebayes
[03:44:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:44:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:44:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:44:10] Found vcfuniq - /usr/local/bin/vcfuniq
[03:44:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:44:10] Found gzip - /bin/gzip
[03:44:10] Found vt - /usr/local/bin/vt
[03:44:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:44:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:44:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:44:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:44:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:44:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:44:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:44:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:07] This is snippy 4.6.0Show full stderr[03:43:07] This is snippy 4.6.0
[03:43:07] Written by Torsten Seemann
[03:43:07] Obtained from https://github.com/tseemann/snippy
[03:43:07] Detected operating system: linux
[03:43:07] Enabling bundled linux tools.
[03:43:07] Found bwa - /usr/local/bin/bwa
[03:43:07] Found bcftools - /usr/local/bin/bcftools
[03:43:07] Found samtools - /usr/local/bin/samtools
[03:43:07] Found java - /usr/local/bin/java
[03:43:07] Found snpEff - /usr/local/bin/snpEff
[03:43:07] Found samclip - /usr/local/bin/samclip
[03:43:07] Found seqtk - /usr/local/bin/seqtk
[03:43:07] Found parallel - /usr/local/bin/parallel
[03:43:07] Found freebayes - /usr/local/bin/freebayes
[03:43:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:07] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:07] Found gzip - /bin/gzip
[03:43:07] Found vt - /usr/local/bin/vt
[03:43:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:43:55] This is snippy 4.6.0Show full stderr[03:43:55] This is snippy 4.6.0
[03:43:55] Written by Torsten Seemann
[03:43:55] Obtained from https://github.com/tseemann/snippy
[03:43:55] Detected operating system: linux
[03:43:55] Enabling bundled linux tools.
[03:43:55] Found bwa - /usr/local/bin/bwa
[03:43:55] Found bcftools - /usr/local/bin/bcftools
[03:43:55] Found samtools - /usr/local/bin/samtools
[03:43:55] Found java - /usr/local/bin/java
[03:43:55] Found snpEff - /usr/local/bin/snpEff
[03:43:55] Found samclip - /usr/local/bin/samclip
[03:43:55] Found seqtk - /usr/local/bin/seqtk
[03:43:55] Found parallel - /usr/local/bin/parallel
[03:43:55] Found freebayes - /usr/local/bin/freebayes
[03:43:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:43:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:43:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:43:55] Found vcfuniq - /usr/local/bin/vcfuniq
[03:43:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:43:55] Found gzip - /bin/gzip
[03:43:55] Found vt - /usr/local/bin/vt
[03:43:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:43:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:43:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:43:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:43:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:43:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:43:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:43:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:44:07] This is snippy 4.6.0Show full stderr[03:44:07] This is snippy 4.6.0
[03:44:07] Written by Torsten Seemann
[03:44:07] Obtained from https://github.com/tseemann/snippy
[03:44:07] Detected operating system: linux
[03:44:07] Enabling bundled linux tools.
[03:44:07] Found bwa - /usr/local/bin/bwa
[03:44:07] Found bcftools - /usr/local/bin/bcftools
[03:44:07] Found samtools - /usr/local/bin/samtools
[03:44:07] Found java - /usr/local/bin/java
[03:44:07] Found snpEff - /usr/local/bin/snpEff
[03:44:07] Found samclip - /usr/local/bin/samclip
[03:44:07] Found seqtk - /usr/local/bin/seqtk
[03:44:07] Found parallel - /usr/local/bin/parallel
[03:44:07] Found freebayes - /usr/local/bin/freebayes
[03:44:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:44:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:44:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:44:07] Found vcfuniq - /usr/local/bin/vcfuniq
[03:44:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:44:07] Found gzip - /bin/gzip
[03:44:07] Found vt - /usr/local/bin/vt
[03:44:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:44:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:44:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:44:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:44:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:44:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:44:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:44:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:57:26] This is snippy 4.6.0Show full stderr[05:57:26] This is snippy 4.6.0
[05:57:26] Written by Torsten Seemann
[05:57:26] Obtained from https://github.com/tseemann/snippy
[05:57:26] Detected operating system: linux
[05:57:26] Enabling bundled linux tools.
[05:57:26] Found bwa - /usr/local/bin/bwa
[05:57:26] Found bcftools - /usr/local/bin/bcftools
[05:57:26] Found samtools - /usr/local/bin/samtools
[05:57:26] Found java - /usr/local/bin/java
[05:57:26] Found snpEff - /usr/local/bin/snpEff
[05:57:26] Found samclip - /usr/local/bin/samclip
[05:57:26] Found seqtk - /usr/local/bin/seqtk
[05:57:26] Found parallel - /usr/local/bin/parallel
[05:57:26] Found freebayes - /usr/local/bin/freebayes
[05:57:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:57:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:57:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:57:26] Found vcfuniq - /usr/local/bin/vcfuniq
[05:57:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:57:26] Found gzip - /bin/gzip
[05:57:26] Found vt - /usr/local/bin/vt
[05:57:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:57:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:57:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:57:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:57:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:57:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:57:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:57:27] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:57:27] Treating reference as 'fasta' format.
[05:57:27] Will use 1 CPU cores.
[05:57:27] Using read file: /corral4/main/objects/0/7/a/dataset_07af536d-eb95-4af9-a0e8-c450eed562e8.dat
[05:57:27] Creating folder: Resistance_27_fasta
[05:57:27] Changing working directory: Resistance_27_fasta
[05:57:27] Creating reference folder: reference
[05:57:27] Extracting FASTA and GFF from reference.
[05:57:28] Wrote 3 sequences to ref.fa
[05:57:28] Wrote 0 features to ref.gff
[05:57:28] Shredding /corral4/main/objects/0/7/a/dataset_07af536d-eb95-4af9-a0e8-c450eed562e8.dat into pseudo-reads
[05:57:32] Wrote 468904 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:57:32] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:57:32] Using BAM RG (Read Group) ID: Resistance_27_fasta
[05:57:32] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:57:33] Running: bwa index reference/ref.fa 2>> snps.log
[05:57:37] Error running command, check Resistance_27_fasta/snps.log |
| 1 | [05:57:59] This is snippy 4.6.0Show full stderr[05:57:59] This is snippy 4.6.0
[05:57:59] Written by Torsten Seemann
[05:57:59] Obtained from https://github.com/tseemann/snippy
[05:57:59] Detected operating system: linux
[05:57:59] Enabling bundled linux tools.
[05:57:59] Found bwa - /usr/local/bin/bwa
[05:57:59] Found bcftools - /usr/local/bin/bcftools
[05:57:59] Found samtools - /usr/local/bin/samtools
[05:57:59] Found java - /usr/local/bin/java
[05:57:59] Found snpEff - /usr/local/bin/snpEff
[05:57:59] Found samclip - /usr/local/bin/samclip
[05:57:59] Found seqtk - /usr/local/bin/seqtk
[05:57:59] Found parallel - /usr/local/bin/parallel
[05:57:59] Found freebayes - /usr/local/bin/freebayes
[05:57:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:57:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:57:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:57:59] Found vcfuniq - /usr/local/bin/vcfuniq
[05:57:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:57:59] Found gzip - /bin/gzip
[05:57:59] Found vt - /usr/local/bin/vt
[05:57:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:57:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:57:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:57:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:57:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:58:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:58:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:58:00] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:58:00] Treating reference as 'fasta' format.
[05:58:00] Will use 1 CPU cores.
[05:58:00] Using read file: /corral4/main/objects/7/1/9/dataset_71939cda-582b-452b-8170-eff2e8633ec7.dat
[05:58:00] Creating folder: Resistance_30_fasta
[05:58:00] Changing working directory: Resistance_30_fasta
[05:58:00] Creating reference folder: reference
[05:58:00] Extracting FASTA and GFF from reference.
[05:58:00] Wrote 3 sequences to ref.fa
[05:58:00] Wrote 0 features to ref.gff
[05:58:00] Shredding /corral4/main/objects/7/1/9/dataset_71939cda-582b-452b-8170-eff2e8633ec7.dat into pseudo-reads
[05:58:04] Wrote 390940 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:58:05] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:58:05] Using BAM RG (Read Group) ID: Resistance_30_fasta
[05:58:05] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:58:05] Running: bwa index reference/ref.fa 2>> snps.log
[05:58:08] Error running command, check Resistance_30_fasta/snps.log |
| 1 | [05:58:28] This is snippy 4.6.0Show full stderr[05:58:28] This is snippy 4.6.0
[05:58:28] Written by Torsten Seemann
[05:58:28] Obtained from https://github.com/tseemann/snippy
[05:58:28] Detected operating system: linux
[05:58:28] Enabling bundled linux tools.
[05:58:28] Found bwa - /usr/local/bin/bwa
[05:58:28] Found bcftools - /usr/local/bin/bcftools
[05:58:28] Found samtools - /usr/local/bin/samtools
[05:58:28] Found java - /usr/local/bin/java
[05:58:28] Found snpEff - /usr/local/bin/snpEff
[05:58:28] Found samclip - /usr/local/bin/samclip
[05:58:28] Found seqtk - /usr/local/bin/seqtk
[05:58:28] Found parallel - /usr/local/bin/parallel
[05:58:28] Found freebayes - /usr/local/bin/freebayes
[05:58:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:58:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:58:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:58:28] Found vcfuniq - /usr/local/bin/vcfuniq
[05:58:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:58:28] Found gzip - /bin/gzip
[05:58:28] Found vt - /usr/local/bin/vt
[05:58:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:58:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:58:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:58:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:58:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:58:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:58:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:58:29] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:58:29] Treating reference as 'fasta' format.
[05:58:29] Will use 1 CPU cores.
[05:58:29] Using read file: /corral4/main/objects/d/f/0/dataset_df046bb5-b8f5-4480-a184-7f83a1019f83.dat
[05:58:29] Creating folder: Resistance_68_fasta
[05:58:29] Changing working directory: Resistance_68_fasta
[05:58:29] Creating reference folder: reference
[05:58:29] Extracting FASTA and GFF from reference.
[05:58:29] Wrote 3 sequences to ref.fa
[05:58:29] Wrote 0 features to ref.gff
[05:58:29] Shredding /corral4/main/objects/d/f/0/dataset_df046bb5-b8f5-4480-a184-7f83a1019f83.dat into pseudo-reads
[05:58:34] Wrote 438110 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:58:34] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:58:34] Using BAM RG (Read Group) ID: Resistance_68_fasta
[05:58:34] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:58:34] Running: bwa index reference/ref.fa 2>> snps.log
[05:58:37] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[05:58:38] Running: ln -sf reference/ref.fa . 2>> snps.log
[05:58:38] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[05:58:38] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[05:58:38] Running: bwa mem -Y -M -R '@RG\tID:Resistance_68_fasta\tSM:Resistance_68_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/258/72258621/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/258/72258621/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/258/72258621/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
|
| 1 | [05:58:32] This is snippy 4.6.0Show full stderr[05:58:32] This is snippy 4.6.0
[05:58:32] Written by Torsten Seemann
[05:58:32] Obtained from https://github.com/tseemann/snippy
[05:58:32] Detected operating system: linux
[05:58:32] Enabling bundled linux tools.
[05:58:32] Found bwa - /usr/local/bin/bwa
[05:58:32] Found bcftools - /usr/local/bin/bcftools
[05:58:32] Found samtools - /usr/local/bin/samtools
[05:58:32] Found java - /usr/local/bin/java
[05:58:32] Found snpEff - /usr/local/bin/snpEff
[05:58:32] Found samclip - /usr/local/bin/samclip
[05:58:32] Found seqtk - /usr/local/bin/seqtk
[05:58:32] Found parallel - /usr/local/bin/parallel
[05:58:32] Found freebayes - /usr/local/bin/freebayes
[05:58:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:58:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:58:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:58:32] Found vcfuniq - /usr/local/bin/vcfuniq
[05:58:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:58:32] Found gzip - /bin/gzip
[05:58:32] Found vt - /usr/local/bin/vt
[05:58:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:58:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:58:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:58:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:58:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:58:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:58:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:58:33] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:58:33] Treating reference as 'fasta' format.
[05:58:33] Will use 1 CPU cores.
[05:58:33] Using read file: /corral4/main/objects/4/b/f/dataset_4bf577f2-77f5-4d64-ad5f-a01e9e27fa4b.dat
[05:58:33] Creating folder: Resistance_69_fasta
[05:58:33] Changing working directory: Resistance_69_fasta
[05:58:33] Creating reference folder: reference
[05:58:33] Extracting FASTA and GFF from reference.
[05:58:34] Wrote 3 sequences to ref.fa
[05:58:34] Wrote 0 features to ref.gff
[05:58:34] Shredding /corral4/main/objects/4/b/f/dataset_4bf577f2-77f5-4d64-ad5f-a01e9e27fa4b.dat into pseudo-reads
[05:58:40] Wrote 400510 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:58:40] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:58:40] Using BAM RG (Read Group) ID: Resistance_69_fasta
[05:58:40] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:58:40] Running: bwa index reference/ref.fa 2>> snps.log
[05:58:40] Error running command, check Resistance_69_fasta/snps.log |
| 1 | [05:59:00] This is snippy 4.6.0Show full stderr[05:59:00] This is snippy 4.6.0
[05:59:00] Written by Torsten Seemann
[05:59:00] Obtained from https://github.com/tseemann/snippy
[05:59:00] Detected operating system: linux
[05:59:00] Enabling bundled linux tools.
[05:59:00] Found bwa - /usr/local/bin/bwa
[05:59:00] Found bcftools - /usr/local/bin/bcftools
[05:59:00] Found samtools - /usr/local/bin/samtools
[05:59:00] Found java - /usr/local/bin/java
[05:59:00] Found snpEff - /usr/local/bin/snpEff
[05:59:00] Found samclip - /usr/local/bin/samclip
[05:59:00] Found seqtk - /usr/local/bin/seqtk
[05:59:00] Found parallel - /usr/local/bin/parallel
[05:59:00] Found freebayes - /usr/local/bin/freebayes
[05:59:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:59:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:59:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:59:00] Found vcfuniq - /usr/local/bin/vcfuniq
[05:59:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:59:00] Found gzip - /bin/gzip
[05:59:00] Found vt - /usr/local/bin/vt
[05:59:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:59:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:59:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:59:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:59:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:59:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:59:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:59:01] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:59:01] Treating reference as 'fasta' format.
[05:59:01] Will use 1 CPU cores.
[05:59:01] Using read file: /corral4/main/objects/7/6/a/dataset_76aadc4d-ac2f-4192-8791-0fe4093b4122.dat
[05:59:01] Creating folder: Resistance_73_fasta
[05:59:01] Changing working directory: Resistance_73_fasta
[05:59:01] Creating reference folder: reference
[05:59:01] Extracting FASTA and GFF from reference.
[05:59:01] Wrote 3 sequences to ref.fa
[05:59:01] Wrote 0 features to ref.gff
[05:59:01] Shredding /corral4/main/objects/7/6/a/dataset_76aadc4d-ac2f-4192-8791-0fe4093b4122.dat into pseudo-reads
[05:59:06] Wrote 415842 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:59:06] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:59:06] Using BAM RG (Read Group) ID: Resistance_73_fasta
[05:59:07] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:59:07] Running: bwa index reference/ref.fa 2>> snps.log
[05:59:11] Error running command, check Resistance_73_fasta/snps.log |
| 1 | [05:53:24] This is snippy 4.6.0Show full stderr[05:53:24] This is snippy 4.6.0
[05:53:24] Written by Torsten Seemann
[05:53:24] Obtained from https://github.com/tseemann/snippy
[05:53:24] Detected operating system: linux
[05:53:24] Enabling bundled linux tools.
[05:53:24] Found bwa - /usr/local/bin/bwa
[05:53:24] Found bcftools - /usr/local/bin/bcftools
[05:53:24] Found samtools - /usr/local/bin/samtools
[05:53:24] Found java - /usr/local/bin/java
[05:53:24] Found snpEff - /usr/local/bin/snpEff
[05:53:24] Found samclip - /usr/local/bin/samclip
[05:53:24] Found seqtk - /usr/local/bin/seqtk
[05:53:24] Found parallel - /usr/local/bin/parallel
[05:53:24] Found freebayes - /usr/local/bin/freebayes
[05:53:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:53:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:53:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:53:24] Found vcfuniq - /usr/local/bin/vcfuniq
[05:53:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:53:24] Found gzip - /bin/gzip
[05:53:24] Found vt - /usr/local/bin/vt
[05:53:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:53:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:53:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:53:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:53:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:53:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:53:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:53:26] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:53:26] Treating reference as 'fasta' format.
[05:53:26] Will use 1 CPU cores.
[05:53:26] Using read file: /corral4/main/objects/4/4/7/dataset_447a024f-c0d7-46ab-a966-b2633c78f043.dat
[05:53:26] Creating folder: Resistance_86_fasta
[05:53:26] Changing working directory: Resistance_86_fasta
[05:53:26] Creating reference folder: reference
[05:53:26] Extracting FASTA and GFF from reference.
[05:53:26] Wrote 3 sequences to ref.fa
[05:53:26] Wrote 0 features to ref.gff
[05:53:26] Shredding /corral4/main/objects/4/4/7/dataset_447a024f-c0d7-46ab-a966-b2633c78f043.dat into pseudo-reads
[05:53:32] Wrote 422132 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:53:32] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:53:32] Using BAM RG (Read Group) ID: Resistance_86_fasta
[05:53:32] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:53:32] Running: bwa index reference/ref.fa 2>> snps.log
[05:53:38] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[05:53:38] Running: ln -sf reference/ref.fa . 2>> snps.log
[05:53:38] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[05:53:38] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[05:53:38] Running: bwa mem -Y -M -R '@RG\tID:Resistance_86_fasta\tSM:Resistance_86_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/258/72258639/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/258/72258639/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/258/72258639/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
|
| 1 | [05:54:28] This is snippy 4.6.0Show full stderr[05:54:28] This is snippy 4.6.0
[05:54:28] Written by Torsten Seemann
[05:54:28] Obtained from https://github.com/tseemann/snippy
[05:54:28] Detected operating system: linux
[05:54:28] Enabling bundled linux tools.
[05:54:28] Found bwa - /usr/local/bin/bwa
[05:54:28] Found bcftools - /usr/local/bin/bcftools
[05:54:28] Found samtools - /usr/local/bin/samtools
[05:54:28] Found java - /usr/local/bin/java
[05:54:28] Found snpEff - /usr/local/bin/snpEff
[05:54:28] Found samclip - /usr/local/bin/samclip
[05:54:28] Found seqtk - /usr/local/bin/seqtk
[05:54:28] Found parallel - /usr/local/bin/parallel
[05:54:28] Found freebayes - /usr/local/bin/freebayes
[05:54:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:54:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:54:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:54:28] Found vcfuniq - /usr/local/bin/vcfuniq
[05:54:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:54:28] Found gzip - /bin/gzip
[05:54:28] Found vt - /usr/local/bin/vt
[05:54:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:54:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:54:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:54:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:54:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:54:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:54:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:54:29] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:54:29] Treating reference as 'fasta' format.
[05:54:29] Will use 1 CPU cores.
[05:54:29] Using read file: /corral4/main/objects/8/2/5/dataset_82599e38-094b-42ab-b0d7-d5e591dc0b91.dat
[05:54:29] Creating folder: Resistance_87_fasta
[05:54:29] Changing working directory: Resistance_87_fasta
[05:54:29] Creating reference folder: reference
[05:54:29] Extracting FASTA and GFF from reference.
[05:54:29] Wrote 3 sequences to ref.fa
[05:54:29] Wrote 0 features to ref.gff
[05:54:29] Shredding /corral4/main/objects/8/2/5/dataset_82599e38-094b-42ab-b0d7-d5e591dc0b91.dat into pseudo-reads
[05:54:34] Wrote 423030 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:54:34] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:54:34] Using BAM RG (Read Group) ID: Resistance_87_fasta
[05:54:34] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:54:34] Running: bwa index reference/ref.fa 2>> snps.log
[05:54:37] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[05:54:37] Running: ln -sf reference/ref.fa . 2>> snps.log
[05:54:37] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[05:54:37] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[05:54:37] Running: bwa mem -Y -M -R '@RG\tID:Resistance_87_fasta\tSM:Resistance_87_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/258/72258640/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/258/72258640/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/258/72258640/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
|
| 1 | [05:55:59] This is snippy 4.6.0Show full stderr[05:55:59] This is snippy 4.6.0
[05:55:59] Written by Torsten Seemann
[05:55:59] Obtained from https://github.com/tseemann/snippy
[05:55:59] Detected operating system: linux
[05:55:59] Enabling bundled linux tools.
[05:55:59] Found bwa - /usr/local/bin/bwa
[05:55:59] Found bcftools - /usr/local/bin/bcftools
[05:55:59] Found samtools - /usr/local/bin/samtools
[05:55:59] Found java - /usr/local/bin/java
[05:55:59] Found snpEff - /usr/local/bin/snpEff
[05:55:59] Found samclip - /usr/local/bin/samclip
[05:55:59] Found seqtk - /usr/local/bin/seqtk
[05:55:59] Found parallel - /usr/local/bin/parallel
[05:55:59] Found freebayes - /usr/local/bin/freebayes
[05:55:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:55:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:55:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:55:59] Found vcfuniq - /usr/local/bin/vcfuniq
[05:55:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:56:00] Found gzip - /bin/gzip
[05:56:00] Found vt - /usr/local/bin/vt
[05:56:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:56:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:56:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:56:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:56:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:56:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:56:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:56:01] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa
[05:56:01] Treating reference as 'fasta' format.
[05:56:01] Will use 1 CPU cores.
[05:56:01] Using read file: /corral4/main/objects/1/b/7/dataset_1b7cfb67-2d85-4140-9a62-51a430d8aa97.dat
[05:56:01] Creating folder: Resistance_89_fasta
[05:56:01] Changing working directory: Resistance_89_fasta
[05:56:01] Creating reference folder: reference
[05:56:01] Extracting FASTA and GFF from reference.
[05:56:01] Wrote 3 sequences to ref.fa
[05:56:01] Wrote 0 features to ref.gff
[05:56:01] Shredding /corral4/main/objects/1/b/7/dataset_1b7cfb67-2d85-4140-9a62-51a430d8aa97.dat into pseudo-reads
[05:56:06] Wrote 411052 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:56:06] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time.
[05:56:06] Using BAM RG (Read Group) ID: Resistance_89_fasta
[05:56:06] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:56:06] Running: bwa index reference/ref.fa 2>> snps.log
[05:56:11] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[05:56:11] Running: ln -sf reference/ref.fa . 2>> snps.log
[05:56:11] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[05:56:11] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[05:56:11] Running: bwa mem -Y -M -R '@RG\tID:Resistance_89_fasta\tSM:Resistance_89_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/258/72258641/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/258/72258641/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/258/72258641/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
|
| 1 | [05:57:12] This is snippy 4.6.0Show full stderr[05:57:12] This is snippy 4.6.0
[05:57:12] Written by Torsten Seemann
[05:57:12] Obtained from https://github.com/tseemann/snippy
[05:57:12] Detected operating system: linux
[05:57:12] Enabling bundled linux tools.
[05:57:12] Found bwa - /usr/local/bin/bwa
[05:57:12] Found bcftools - /usr/local/bin/bcftools
[05:57:12] Found samtools - /usr/local/bin/samtools
[05:57:12] Found java - /usr/local/bin/java
[05:57:12] Found snpEff - /usr/local/bin/snpEff
[05:57:12] Found samclip - /usr/local/bin/samclip
[05:57:12] Found seqtk - /usr/local/bin/seqtk
[05:57:12] Found parallel - /usr/local/bin/parallel
[05:57:12] Found freebayes - /usr/local/bin/freebayes
[05:57:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:57:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:57:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:57:12] Found vcfuniq - /usr/local/bin/vcfuniq
[05:57:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:57:12] Found gzip - /bin/gzip
[05:57:12] Found vt - /usr/local/bin/vt
[05:57:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:57:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:57:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:57:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:57:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:57:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:57:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:57:14] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:57:14] Treating reference as 'fasta' format.
[05:57:14] Will use 1 CPU cores.
[05:57:14] Using read file: /corral4/main/objects/b/4/b/dataset_b4b28949-0cba-496c-9eba-8bb6e332013e.dat
[05:57:14] Creating folder: GCF_005144725_1_ASM514472v1_genomic_fna
[05:57:14] Changing working directory: GCF_005144725_1_ASM514472v1_genomic_fna
[05:57:14] Creating reference folder: reference
[05:57:14] Extracting FASTA and GFF from reference.
[05:57:15] Wrote 1 sequences to ref.fa
[05:57:15] Wrote 0 features to ref.gff
[05:57:15] Shredding /corral4/main/objects/b/4/b/dataset_b4b28949-0cba-496c-9eba-8bb6e332013e.dat into pseudo-reads
[05:57:18] Wrote 355626 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:57:18] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time.
[05:57:18] Using BAM RG (Read Group) ID: GCF_005144725_1_ASM514472v1_genomic_fna
[05:57:18] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:57:19] Running: bwa index reference/ref.fa 2>> snps.log
[05:57:24] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[05:57:24] Running: ln -sf reference/ref.fa . 2>> snps.log
[05:57:24] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[05:57:24] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[05:57:24] Running: bwa mem -Y -M -R '@RG\tID:GCF_005144725_1_ASM514472v1_genomic_fna\tSM:GCF_005144725_1_ASM514472v1_genomic_fna' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/260/72260487/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/260/72260487/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/260/72260487/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] |
| 1 | [05:56:35] This is snippy 4.6.0Show full stderr[05:56:35] This is snippy 4.6.0
[05:56:35] Written by Torsten Seemann
[05:56:35] Obtained from https://github.com/tseemann/snippy
[05:56:35] Detected operating system: linux
[05:56:35] Enabling bundled linux tools.
[05:56:35] Found bwa - /usr/local/bin/bwa
[05:56:35] Found bcftools - /usr/local/bin/bcftools
[05:56:35] Found samtools - /usr/local/bin/samtools
[05:56:35] Found java - /usr/local/bin/java
[05:56:35] Found snpEff - /usr/local/bin/snpEff
[05:56:35] Found samclip - /usr/local/bin/samclip
[05:56:35] Found seqtk - /usr/local/bin/seqtk
[05:56:35] Found parallel - /usr/local/bin/parallel
[05:56:35] Found freebayes - /usr/local/bin/freebayes
[05:56:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:56:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:56:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:56:35] Found vcfuniq - /usr/local/bin/vcfuniq
[05:56:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:56:35] Found gzip - /bin/gzip
[05:56:35] Found vt - /usr/local/bin/vt
[05:56:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:56:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:56:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:56:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:56:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:56:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:56:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:56:36] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:56:36] Treating reference as 'fasta' format.
[05:56:36] Will use 1 CPU cores.
[05:56:36] Using read file: /corral4/main/objects/4/c/6/dataset_4c6552aa-c652-4a08-9a51-7d0c28a4126a.dat
[05:56:36] Creating folder: GCA_019661335_1_ASM1966133v1_genomic_fna
[05:56:36] Changing working directory: GCA_019661335_1_ASM1966133v1_genomic_fna
[05:56:36] Creating reference folder: reference
[05:56:36] Extracting FASTA and GFF from reference.
[05:56:36] Wrote 1 sequences to ref.fa
[05:56:36] Wrote 0 features to ref.gff
[05:56:36] Shredding /corral4/main/objects/4/c/6/dataset_4c6552aa-c652-4a08-9a51-7d0c28a4126a.dat into pseudo-reads
[05:56:40] Wrote 436000 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:56:40] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time.
[05:56:40] Using BAM RG (Read Group) ID: GCA_019661335_1_ASM1966133v1_genomic_fna
[05:56:40] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:56:40] Running: bwa index reference/ref.fa 2>> snps.log
[05:56:42] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[05:56:42] Running: ln -sf reference/ref.fa . 2>> snps.log
[05:56:42] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[05:56:42] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[05:56:42] Running: bwa mem -Y -M -R '@RG\tID:GCA_019661335_1_ASM1966133v1_genomic_fna\tSM:GCA_019661335_1_ASM1966133v1_genomic_fna' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/260/72260519/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/260/72260519/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/260/72260519/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[sam |
| 1 | [05:58:10] This is snippy 4.6.0Show full stderr[05:58:10] This is snippy 4.6.0
[05:58:10] Written by Torsten Seemann
[05:58:10] Obtained from https://github.com/tseemann/snippy
[05:58:10] Detected operating system: linux
[05:58:10] Enabling bundled linux tools.
[05:58:10] Found bwa - /usr/local/bin/bwa
[05:58:10] Found bcftools - /usr/local/bin/bcftools
[05:58:10] Found samtools - /usr/local/bin/samtools
[05:58:10] Found java - /usr/local/bin/java
[05:58:10] Found snpEff - /usr/local/bin/snpEff
[05:58:10] Found samclip - /usr/local/bin/samclip
[05:58:10] Found seqtk - /usr/local/bin/seqtk
[05:58:10] Found parallel - /usr/local/bin/parallel
[05:58:10] Found freebayes - /usr/local/bin/freebayes
[05:58:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:58:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:58:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:58:10] Found vcfuniq - /usr/local/bin/vcfuniq
[05:58:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:58:10] Found gzip - /bin/gzip
[05:58:10] Found vt - /usr/local/bin/vt
[05:58:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:58:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:58:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:58:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:58:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:58:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:58:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:58:11] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:58:11] Treating reference as 'fasta' format.
[05:58:11] Will use 1 CPU cores.
[05:58:11] Using read file: /corral4/main/objects/3/9/4/dataset_3947c198-e6d1-4c51-8840-17091505addc.dat
[05:58:11] Creating folder: GCA_019661385_1_ASM1966138v1_genomic_fna
[05:58:11] Changing working directory: GCA_019661385_1_ASM1966138v1_genomic_fna
[05:58:11] Creating reference folder: reference
[05:58:11] Extracting FASTA and GFF from reference.
[05:58:11] Wrote 1 sequences to ref.fa
[05:58:11] Wrote 0 features to ref.gff
[05:58:11] Shredding /corral4/main/objects/3/9/4/dataset_3947c198-e6d1-4c51-8840-17091505addc.dat into pseudo-reads
[05:58:16] Wrote 447600 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:58:16] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[05:58:16] Using BAM RG (Read Group) ID: GCA_019661385_1_ASM1966138v1_genomic_fna
[05:58:16] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:58:16] Error running command, check GCA_019661385_1_ASM1966138v1_genomic_fna/snps.log |
| 1 | [05:59:38] This is snippy 4.6.0Show full stderr[05:59:38] This is snippy 4.6.0
[05:59:38] Written by Torsten Seemann
[05:59:38] Obtained from https://github.com/tseemann/snippy
[05:59:38] Detected operating system: linux
[05:59:38] Enabling bundled linux tools.
[05:59:38] Found bwa - /usr/local/bin/bwa
[05:59:38] Found bcftools - /usr/local/bin/bcftools
[05:59:38] Found samtools - /usr/local/bin/samtools
[05:59:38] Found java - /usr/local/bin/java
[05:59:38] Found snpEff - /usr/local/bin/snpEff
[05:59:38] Found samclip - /usr/local/bin/samclip
[05:59:38] Found seqtk - /usr/local/bin/seqtk
[05:59:38] Found parallel - /usr/local/bin/parallel
[05:59:38] Found freebayes - /usr/local/bin/freebayes
[05:59:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:59:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:59:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:59:38] Found vcfuniq - /usr/local/bin/vcfuniq
[05:59:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:59:38] Found gzip - /bin/gzip
[05:59:38] Found vt - /usr/local/bin/vt
[05:59:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:59:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:59:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:59:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:59:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:59:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:59:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:59:39] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:59:39] Treating reference as 'fasta' format.
[05:59:39] Will use 1 CPU cores.
[05:59:39] Using read file: /corral4/main/objects/5/0/e/dataset_50ebb9d0-52f7-47f9-b652-9c2be03cc94c.dat
[05:59:39] Creating folder: GCF_002447215_1_ASM244721v1_genomic_fna
[05:59:39] Changing working directory: GCF_002447215_1_ASM244721v1_genomic_fna
[05:59:39] Creating reference folder: reference
[05:59:39] Extracting FASTA and GFF from reference.
[05:59:39] Wrote 1 sequences to ref.fa
[05:59:39] Wrote 0 features to ref.gff
[05:59:39] Shredding /corral4/main/objects/5/0/e/dataset_50ebb9d0-52f7-47f9-b652-9c2be03cc94c.dat into pseudo-reads
[05:59:43] Wrote 352948 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:59:43] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[05:59:43] Using BAM RG (Read Group) ID: GCF_002447215_1_ASM244721v1_genomic_fna
[05:59:43] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:59:43] Error running command, check GCF_002447215_1_ASM244721v1_genomic_fna/snps.log |
| 1 | [05:55:53] This is snippy 4.6.0Show full stderr[05:55:53] This is snippy 4.6.0
[05:55:53] Written by Torsten Seemann
[05:55:53] Obtained from https://github.com/tseemann/snippy
[05:55:53] Detected operating system: linux
[05:55:53] Enabling bundled linux tools.
[05:55:53] Found bwa - /usr/local/bin/bwa
[05:55:53] Found bcftools - /usr/local/bin/bcftools
[05:55:53] Found samtools - /usr/local/bin/samtools
[05:55:53] Found java - /usr/local/bin/java
[05:55:53] Found snpEff - /usr/local/bin/snpEff
[05:55:53] Found samclip - /usr/local/bin/samclip
[05:55:53] Found seqtk - /usr/local/bin/seqtk
[05:55:53] Found parallel - /usr/local/bin/parallel
[05:55:53] Found freebayes - /usr/local/bin/freebayes
[05:55:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:55:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:55:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:55:53] Found vcfuniq - /usr/local/bin/vcfuniq
[05:55:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:55:53] Found gzip - /bin/gzip
[05:55:53] Found vt - /usr/local/bin/vt
[05:55:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:55:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:55:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:55:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:55:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:55:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:55:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:55:55] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:55:55] Treating reference as 'fasta' format.
[05:55:55] Will use 1 CPU cores.
[05:55:55] Using read file: /corral4/main/objects/7/6/a/dataset_76a18bff-8cf6-43ba-94b7-fbb3d96ef5fa.dat
[05:55:55] Creating folder: GCF_003006135_1_ASM300613v1_genomic_fna
[05:55:55] Changing working directory: GCF_003006135_1_ASM300613v1_genomic_fna
[05:55:55] Creating reference folder: reference
[05:55:55] Extracting FASTA and GFF from reference.
[05:55:55] Wrote 1 sequences to ref.fa
[05:55:55] Wrote 0 features to ref.gff
[05:55:55] Shredding /corral4/main/objects/7/6/a/dataset_76a18bff-8cf6-43ba-94b7-fbb3d96ef5fa.dat into pseudo-reads
[05:55:59] Wrote 353138 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:55:59] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time.
[05:55:59] Using BAM RG (Read Group) ID: GCF_003006135_1_ASM300613v1_genomic_fna
[05:55:59] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:55:59] Running: bwa index reference/ref.fa 2>> snps.log
[05:56:04] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[05:56:04] Running: ln -sf reference/ref.fa . 2>> snps.log
[05:56:04] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[05:56:04] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[05:56:04] Running: bwa mem -Y -M -R '@RG\tID:GCF_003006135_1_ASM300613v1_genomic_fna\tSM:GCF_003006135_1_ASM300613v1_genomic_fna' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/260/72260549/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/260/72260549/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/260/72260549/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] |
| 1 | [05:57:53] This is snippy 4.6.0Show full stderr[05:57:53] This is snippy 4.6.0
[05:57:53] Written by Torsten Seemann
[05:57:53] Obtained from https://github.com/tseemann/snippy
[05:57:53] Detected operating system: linux
[05:57:53] Enabling bundled linux tools.
[05:57:53] Found bwa - /usr/local/bin/bwa
[05:57:53] Found bcftools - /usr/local/bin/bcftools
[05:57:53] Found samtools - /usr/local/bin/samtools
[05:57:53] Found java - /usr/local/bin/java
[05:57:53] Found snpEff - /usr/local/bin/snpEff
[05:57:53] Found samclip - /usr/local/bin/samclip
[05:57:53] Found seqtk - /usr/local/bin/seqtk
[05:57:53] Found parallel - /usr/local/bin/parallel
[05:57:53] Found freebayes - /usr/local/bin/freebayes
[05:57:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:57:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:57:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:57:53] Found vcfuniq - /usr/local/bin/vcfuniq
[05:57:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:57:53] Found gzip - /bin/gzip
[05:57:53] Found vt - /usr/local/bin/vt
[05:57:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:57:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:57:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:57:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:57:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:57:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:57:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:57:54] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:57:54] Treating reference as 'fasta' format.
[05:57:54] Will use 1 CPU cores.
[05:57:54] Using read file: /corral4/main/objects/0/5/e/dataset_05e984c9-f75e-41a8-add8-d623160bf91e.dat
[05:57:54] Creating folder: GCF_002591875_1_ASM259187v1_genomic_fna
[05:57:54] Changing working directory: GCF_002591875_1_ASM259187v1_genomic_fna
[05:57:54] Creating reference folder: reference
[05:57:54] Extracting FASTA and GFF from reference.
[05:57:54] Wrote 1 sequences to ref.fa
[05:57:54] Wrote 0 features to ref.gff
[05:57:54] Shredding /corral4/main/objects/0/5/e/dataset_05e984c9-f75e-41a8-add8-d623160bf91e.dat into pseudo-reads
[05:57:58] Wrote 351844 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:57:58] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time.
[05:57:58] Using BAM RG (Read Group) ID: GCF_002591875_1_ASM259187v1_genomic_fna
[05:57:58] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:57:58] Running: bwa index reference/ref.fa 2>> snps.log
[05:58:01] Error running command, check GCF_002591875_1_ASM259187v1_genomic_fna/snps.log |
| 1 | [05:56:15] This is snippy 4.6.0Show full stderr[05:56:15] This is snippy 4.6.0
[05:56:15] Written by Torsten Seemann
[05:56:15] Obtained from https://github.com/tseemann/snippy
[05:56:15] Detected operating system: linux
[05:56:15] Enabling bundled linux tools.
[05:56:15] Found bwa - /usr/local/bin/bwa
[05:56:15] Found bcftools - /usr/local/bin/bcftools
[05:56:15] Found samtools - /usr/local/bin/samtools
[05:56:15] Found java - /usr/local/bin/java
[05:56:15] Found snpEff - /usr/local/bin/snpEff
[05:56:15] Found samclip - /usr/local/bin/samclip
[05:56:15] Found seqtk - /usr/local/bin/seqtk
[05:56:15] Found parallel - /usr/local/bin/parallel
[05:56:15] Found freebayes - /usr/local/bin/freebayes
[05:56:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:56:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:56:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:56:15] Found vcfuniq - /usr/local/bin/vcfuniq
[05:56:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:56:15] Found gzip - /bin/gzip
[05:56:15] Found vt - /usr/local/bin/vt
[05:56:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:56:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:56:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:56:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:56:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:56:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:56:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:56:17] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:56:17] Treating reference as 'fasta' format.
[05:56:17] Will use 1 CPU cores.
[05:56:17] Using read file: /corral4/main/objects/4/7/9/dataset_479374ce-f6f8-4112-9293-78fcdc1cb420.dat
[05:56:17] Creating folder: GCF_002447275_1_ASM244727v1_genomic_fna
[05:56:17] Changing working directory: GCF_002447275_1_ASM244727v1_genomic_fna
[05:56:17] Creating reference folder: reference
[05:56:17] Extracting FASTA and GFF from reference.
[05:56:17] Wrote 1 sequences to ref.fa
[05:56:17] Wrote 0 features to ref.gff
[05:56:17] Shredding /corral4/main/objects/4/7/9/dataset_479374ce-f6f8-4112-9293-78fcdc1cb420.dat into pseudo-reads
[05:56:23] Wrote 352954 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:56:23] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time.
[05:56:23] Using BAM RG (Read Group) ID: GCF_002447275_1_ASM244727v1_genomic_fna
[05:56:23] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:56:23] Running: bwa index reference/ref.fa 2>> snps.log
[05:56:28] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[05:56:28] Running: ln -sf reference/ref.fa . 2>> snps.log
[05:56:28] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[05:56:28] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[05:56:28] Running: bwa mem -Y -M -R '@RG\tID:GCF_002447275_1_ASM244727v1_genomic_fna\tSM:GCF_002447275_1_ASM244727v1_genomic_fna' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/260/72260554/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/260/72260554/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/260/72260554/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] |
| 1 | [05:57:34] This is snippy 4.6.0Show full stderr[05:57:34] This is snippy 4.6.0
[05:57:34] Written by Torsten Seemann
[05:57:34] Obtained from https://github.com/tseemann/snippy
[05:57:34] Detected operating system: linux
[05:57:34] Enabling bundled linux tools.
[05:57:34] Found bwa - /usr/local/bin/bwa
[05:57:34] Found bcftools - /usr/local/bin/bcftools
[05:57:34] Found samtools - /usr/local/bin/samtools
[05:57:34] Found java - /usr/local/bin/java
[05:57:34] Found snpEff - /usr/local/bin/snpEff
[05:57:34] Found samclip - /usr/local/bin/samclip
[05:57:34] Found seqtk - /usr/local/bin/seqtk
[05:57:34] Found parallel - /usr/local/bin/parallel
[05:57:34] Found freebayes - /usr/local/bin/freebayes
[05:57:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:57:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:57:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:57:34] Found vcfuniq - /usr/local/bin/vcfuniq
[05:57:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:57:34] Found gzip - /bin/gzip
[05:57:34] Found vt - /usr/local/bin/vt
[05:57:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:57:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:57:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:57:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:57:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:57:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:57:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:57:36] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:57:36] Treating reference as 'fasta' format.
[05:57:36] Will use 1 CPU cores.
[05:57:36] Using read file: /corral4/main/objects/7/7/3/dataset_7738437a-e1ae-4a91-812c-b3134eae84a7.dat
[05:57:36] Creating folder: GCA_007989945_1_ASM798994v1_genomic_fna
[05:57:36] Changing working directory: GCA_007989945_1_ASM798994v1_genomic_fna
[05:57:36] Creating reference folder: reference
[05:57:36] Extracting FASTA and GFF from reference.
[05:57:36] Wrote 1 sequences to ref.fa
[05:57:36] Wrote 0 features to ref.gff
[05:57:36] Shredding /corral4/main/objects/7/7/3/dataset_7738437a-e1ae-4a91-812c-b3134eae84a7.dat into pseudo-reads
[05:57:43] Wrote 443378 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:57:43] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time.
[05:57:43] Using BAM RG (Read Group) ID: GCA_007989945_1_ASM798994v1_genomic_fna
[05:57:43] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:57:43] Running: bwa index reference/ref.fa 2>> snps.log
[05:57:47] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[05:57:47] Running: ln -sf reference/ref.fa . 2>> snps.log
[05:57:47] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[05:57:47] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[05:57:47] Running: bwa mem -Y -M -R '@RG\tID:GCA_007989945_1_ASM798994v1_genomic_fna\tSM:GCA_007989945_1_ASM798994v1_genomic_fna' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/260/72260555/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/260/72260555/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/260/72260555/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] |
| 1 | [05:59:02] This is snippy 4.6.0Show full stderr[05:59:02] This is snippy 4.6.0
[05:59:02] Written by Torsten Seemann
[05:59:02] Obtained from https://github.com/tseemann/snippy
[05:59:02] Detected operating system: linux
[05:59:02] Enabling bundled linux tools.
[05:59:02] Found bwa - /usr/local/bin/bwa
[05:59:02] Found bcftools - /usr/local/bin/bcftools
[05:59:02] Found samtools - /usr/local/bin/samtools
[05:59:02] Found java - /usr/local/bin/java
[05:59:02] Found snpEff - /usr/local/bin/snpEff
[05:59:02] Found samclip - /usr/local/bin/samclip
[05:59:02] Found seqtk - /usr/local/bin/seqtk
[05:59:02] Found parallel - /usr/local/bin/parallel
[05:59:02] Found freebayes - /usr/local/bin/freebayes
[05:59:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:59:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:59:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:59:02] Found vcfuniq - /usr/local/bin/vcfuniq
[05:59:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:59:02] Found gzip - /bin/gzip
[05:59:02] Found vt - /usr/local/bin/vt
[05:59:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:59:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:59:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:59:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:59:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:59:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:59:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:59:03] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:59:03] Treating reference as 'fasta' format.
[05:59:03] Will use 1 CPU cores.
[05:59:03] Using read file: /corral4/main/objects/8/d/c/dataset_8dce7616-b304-4131-b366-2c3659c915c1.dat
[05:59:03] Creating folder: GCF_028583285_1_ASM2858328v1_genomic_fna
[05:59:03] Changing working directory: GCF_028583285_1_ASM2858328v1_genomic_fna
[05:59:03] Creating reference folder: reference
[05:59:03] Extracting FASTA and GFF from reference.
[05:59:03] Wrote 1 sequences to ref.fa
[05:59:03] Wrote 0 features to ref.gff
[05:59:03] Shredding /corral4/main/objects/8/d/c/dataset_8dce7616-b304-4131-b366-2c3659c915c1.dat into pseudo-reads
[05:59:06] Wrote 347480 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:59:06] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time.
[05:59:06] Using BAM RG (Read Group) ID: GCF_028583285_1_ASM2858328v1_genomic_fna
[05:59:06] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:59:06] Running: bwa index reference/ref.fa 2>> snps.log
[05:59:07] Error running command, check GCF_028583285_1_ASM2858328v1_genomic_fna/snps.log |
| 1 | [05:59:52] This is snippy 4.6.0Show full stderr[05:59:52] This is snippy 4.6.0
[05:59:52] Written by Torsten Seemann
[05:59:52] Obtained from https://github.com/tseemann/snippy
[05:59:52] Detected operating system: linux
[05:59:52] Enabling bundled linux tools.
[05:59:52] Found bwa - /usr/local/bin/bwa
[05:59:52] Found bcftools - /usr/local/bin/bcftools
[05:59:52] Found samtools - /usr/local/bin/samtools
[05:59:52] Found java - /usr/local/bin/java
[05:59:52] Found snpEff - /usr/local/bin/snpEff
[05:59:52] Found samclip - /usr/local/bin/samclip
[05:59:52] Found seqtk - /usr/local/bin/seqtk
[05:59:52] Found parallel - /usr/local/bin/parallel
[05:59:52] Found freebayes - /usr/local/bin/freebayes
[05:59:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:59:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:59:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:59:52] Found vcfuniq - /usr/local/bin/vcfuniq
[05:59:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:59:52] Found gzip - /bin/gzip
[05:59:52] Found vt - /usr/local/bin/vt
[05:59:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:59:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:59:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:59:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:59:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:59:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:59:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:59:53] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[05:59:53] Treating reference as 'fasta' format.
[05:59:53] Will use 1 CPU cores.
[05:59:53] Using read file: /corral4/main/objects/e/4/5/dataset_e45e5d48-2705-4eb4-a604-0eba278aadf1.dat
[05:59:53] Creating folder: GCF_903992765_1_Q1141_genomic_fna
[05:59:53] Changing working directory: GCF_903992765_1_Q1141_genomic_fna
[05:59:53] Creating reference folder: reference
[05:59:53] Extracting FASTA and GFF from reference.
[05:59:53] Wrote 1 sequences to ref.fa
[05:59:53] Wrote 0 features to ref.gff
[05:59:53] Shredding /corral4/main/objects/e/4/5/dataset_e45e5d48-2705-4eb4-a604-0eba278aadf1.dat into pseudo-reads
[05:59:57] Wrote 353492 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[05:59:57] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[05:59:57] Using BAM RG (Read Group) ID: GCF_903992765_1_Q1141_genomic_fna
[05:59:57] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:59:57] Error running command, check GCF_903992765_1_Q1141_genomic_fna/snps.log |
| 1 | [06:00:26] This is snippy 4.6.0Show full stderr[06:00:26] This is snippy 4.6.0
[06:00:26] Written by Torsten Seemann
[06:00:26] Obtained from https://github.com/tseemann/snippy
[06:00:26] Detected operating system: linux
[06:00:26] Enabling bundled linux tools.
[06:00:26] Found bwa - /usr/local/bin/bwa
[06:00:26] Found bcftools - /usr/local/bin/bcftools
[06:00:26] Found samtools - /usr/local/bin/samtools
[06:00:26] Found java - /usr/local/bin/java
[06:00:26] Found snpEff - /usr/local/bin/snpEff
[06:00:26] Found samclip - /usr/local/bin/samclip
[06:00:26] Found seqtk - /usr/local/bin/seqtk
[06:00:26] Found parallel - /usr/local/bin/parallel
[06:00:26] Found freebayes - /usr/local/bin/freebayes
[06:00:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:00:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:00:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:00:26] Found vcfuniq - /usr/local/bin/vcfuniq
[06:00:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:00:26] Found gzip - /bin/gzip
[06:00:26] Found vt - /usr/local/bin/vt
[06:00:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:00:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:00:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:00:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:00:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:00:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:00:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:00:26] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[06:00:26] Treating reference as 'fasta' format.
[06:00:26] Will use 1 CPU cores.
[06:00:27] Using read file: /corral4/main/objects/4/1/5/dataset_415e26e2-7ee6-4697-9f0c-796e1a5722b6.dat
[06:00:27] Creating folder: GCF_902506675_1_P9978_genomic_fna
[06:00:27] Changing working directory: GCF_902506675_1_P9978_genomic_fna
[06:00:27] Creating reference folder: reference
[06:00:27] Extracting FASTA and GFF from reference.
[06:00:27] Wrote 1 sequences to ref.fa
[06:00:27] Wrote 0 features to ref.gff
[06:00:27] Shredding /corral4/main/objects/4/1/5/dataset_415e26e2-7ee6-4697-9f0c-796e1a5722b6.dat into pseudo-reads
[06:00:30] Wrote 349272 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[06:00:30] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[06:00:30] Using BAM RG (Read Group) ID: GCF_902506675_1_P9978_genomic_fna
[06:00:30] Running: samtools faidx reference/ref.fa 2>> snps.log
[06:00:30] Error running command, check GCF_902506675_1_P9978_genomic_fna/snps.log |
| 1 | [06:00:13] This is snippy 4.6.0Show full stderr[06:00:13] This is snippy 4.6.0
[06:00:13] Written by Torsten Seemann
[06:00:13] Obtained from https://github.com/tseemann/snippy
[06:00:13] Detected operating system: linux
[06:00:13] Enabling bundled linux tools.
[06:00:13] Found bwa - /usr/local/bin/bwa
[06:00:13] Found bcftools - /usr/local/bin/bcftools
[06:00:13] Found samtools - /usr/local/bin/samtools
[06:00:13] Found java - /usr/local/bin/java
[06:00:13] Found snpEff - /usr/local/bin/snpEff
[06:00:13] Found samclip - /usr/local/bin/samclip
[06:00:13] Found seqtk - /usr/local/bin/seqtk
[06:00:13] Found parallel - /usr/local/bin/parallel
[06:00:13] Found freebayes - /usr/local/bin/freebayes
[06:00:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:00:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:00:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:00:13] Found vcfuniq - /usr/local/bin/vcfuniq
[06:00:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:00:13] Found gzip - /bin/gzip
[06:00:13] Found vt - /usr/local/bin/vt
[06:00:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:00:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:00:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:00:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:00:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:00:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:00:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:00:14] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[06:00:14] Treating reference as 'fasta' format.
[06:00:14] Will use 1 CPU cores.
[06:00:15] Using read file: /corral4/main/objects/f/9/9/dataset_f995321f-8b51-4ecb-805f-86b0ba5540fe.dat
[06:00:15] Creating folder: GCF_902506635_1_P9981_genomic_fna
[06:00:15] Changing working directory: GCF_902506635_1_P9981_genomic_fna
[06:00:15] Creating reference folder: reference
[06:00:15] Extracting FASTA and GFF from reference.
[06:00:15] Wrote 1 sequences to ref.fa
[06:00:15] Wrote 0 features to ref.gff
[06:00:15] Shredding /corral4/main/objects/f/9/9/dataset_f995321f-8b51-4ecb-805f-86b0ba5540fe.dat into pseudo-reads
[06:00:18] Wrote 348054 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[06:00:18] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[06:00:18] Using BAM RG (Read Group) ID: GCF_902506635_1_P9981_genomic_fna
[06:00:18] Running: samtools faidx reference/ref.fa 2>> snps.log
[06:00:18] Error running command, check GCF_902506635_1_P9981_genomic_fna/snps.log |
| 1 | [06:00:33] This is snippy 4.6.0Show full stderr[06:00:33] This is snippy 4.6.0
[06:00:33] Written by Torsten Seemann
[06:00:33] Obtained from https://github.com/tseemann/snippy
[06:00:33] Detected operating system: linux
[06:00:33] Enabling bundled linux tools.
[06:00:33] Found bwa - /usr/local/bin/bwa
[06:00:33] Found bcftools - /usr/local/bin/bcftools
[06:00:33] Found samtools - /usr/local/bin/samtools
[06:00:33] Found java - /usr/local/bin/java
[06:00:33] Found snpEff - /usr/local/bin/snpEff
[06:00:33] Found samclip - /usr/local/bin/samclip
[06:00:33] Found seqtk - /usr/local/bin/seqtk
[06:00:33] Found parallel - /usr/local/bin/parallel
[06:00:33] Found freebayes - /usr/local/bin/freebayes
[06:00:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:00:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:00:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:00:33] Found vcfuniq - /usr/local/bin/vcfuniq
[06:00:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:00:33] Found gzip - /bin/gzip
[06:00:33] Found vt - /usr/local/bin/vt
[06:00:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:00:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:00:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:00:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:00:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:00:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:00:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:00:34] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[06:00:34] Treating reference as 'fasta' format.
[06:00:34] Will use 1 CPU cores.
[06:00:34] Using read file: /corral4/main/objects/f/4/a/dataset_f4a300b2-ef58-46df-814b-98824da69192.dat
[06:00:34] Creating folder: GCF_011392525_1_ASM1139252v1_genomic_fna
[06:00:34] Changing working directory: GCF_011392525_1_ASM1139252v1_genomic_fna
[06:00:34] Creating reference folder: reference
[06:00:34] Extracting FASTA and GFF from reference.
[06:00:34] Wrote 1 sequences to ref.fa
[06:00:34] Wrote 0 features to ref.gff
[06:00:34] Shredding /corral4/main/objects/f/4/a/dataset_f4a300b2-ef58-46df-814b-98824da69192.dat into pseudo-reads
[06:00:37] Wrote 365008 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[06:00:37] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[06:00:37] Using BAM RG (Read Group) ID: GCF_011392525_1_ASM1139252v1_genomic_fna
[06:00:37] Running: samtools faidx reference/ref.fa 2>> snps.log
[06:00:37] Error running command, check GCF_011392525_1_ASM1139252v1_genomic_fna/snps.log |
| 1 | [06:00:29] This is snippy 4.6.0Show full stderr[06:00:29] This is snippy 4.6.0
[06:00:29] Written by Torsten Seemann
[06:00:29] Obtained from https://github.com/tseemann/snippy
[06:00:29] Detected operating system: linux
[06:00:29] Enabling bundled linux tools.
[06:00:29] Found bwa - /usr/local/bin/bwa
[06:00:29] Found bcftools - /usr/local/bin/bcftools
[06:00:29] Found samtools - /usr/local/bin/samtools
[06:00:29] Found java - /usr/local/bin/java
[06:00:29] Found snpEff - /usr/local/bin/snpEff
[06:00:29] Found samclip - /usr/local/bin/samclip
[06:00:29] Found seqtk - /usr/local/bin/seqtk
[06:00:29] Found parallel - /usr/local/bin/parallel
[06:00:29] Found freebayes - /usr/local/bin/freebayes
[06:00:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:00:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:00:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:00:29] Found vcfuniq - /usr/local/bin/vcfuniq
[06:00:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:00:29] Found gzip - /bin/gzip
[06:00:29] Found vt - /usr/local/bin/vt
[06:00:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:00:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:00:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:00:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:00:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:00:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:00:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:00:30] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[06:00:30] Treating reference as 'fasta' format.
[06:00:30] Will use 1 CPU cores.
[06:00:30] Using read file: /corral4/main/objects/e/9/7/dataset_e97c768b-202c-4835-a61e-ec62a693b7f2.dat
[06:00:30] Creating folder: GCF_008033095_1_ASM803309v1_genomic_fna
[06:00:30] Changing working directory: GCF_008033095_1_ASM803309v1_genomic_fna
[06:00:30] Creating reference folder: reference
[06:00:30] Extracting FASTA and GFF from reference.
[06:00:30] Wrote 1 sequences to ref.fa
[06:00:30] Wrote 0 features to ref.gff
[06:00:30] Shredding /corral4/main/objects/e/9/7/dataset_e97c768b-202c-4835-a61e-ec62a693b7f2.dat into pseudo-reads
[06:00:33] Wrote 348034 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[06:00:33] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[06:00:33] Using BAM RG (Read Group) ID: GCF_008033095_1_ASM803309v1_genomic_fna
[06:00:33] Running: samtools faidx reference/ref.fa 2>> snps.log
[06:00:33] Error running command, check GCF_008033095_1_ASM803309v1_genomic_fna/snps.log |
| 1 | [07:02:28] This is snippy 4.6.0Show full stderr[07:02:28] This is snippy 4.6.0
[07:02:28] Written by Torsten Seemann
[07:02:28] Obtained from https://github.com/tseemann/snippy
[07:02:28] Detected operating system: linux
[07:02:28] Enabling bundled linux tools.
[07:02:28] Found bwa - /usr/local/bin/bwa
[07:02:28] Found bcftools - /usr/local/bin/bcftools
[07:02:28] Found samtools - /usr/local/bin/samtools
[07:02:28] Found java - /usr/local/bin/java
[07:02:28] Found snpEff - /usr/local/bin/snpEff
[07:02:28] Found samclip - /usr/local/bin/samclip
[07:02:28] Found seqtk - /usr/local/bin/seqtk
[07:02:28] Found parallel - /usr/local/bin/parallel
[07:02:28] Found freebayes - /usr/local/bin/freebayes
[07:02:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:02:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:02:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:02:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:02:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:02:28] Found gzip - /bin/gzip
[07:02:28] Found vt - /usr/local/bin/vt
[07:02:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:02:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:02:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:02:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:02:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:02:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:02:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:02:29] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:02:29] Treating reference as 'fasta' format.
[07:02:29] Will use 1 CPU cores.
[07:02:29] Using read file: /corral4/main/objects/3/9/7/dataset_3976135c-0036-4694-8aea-44389097c194.dat
[07:02:29] Creating folder: BVBRC_genome_sequence__83__fasta
[07:02:29] Changing working directory: BVBRC_genome_sequence__83__fasta
[07:02:29] Creating reference folder: reference
[07:02:29] Extracting FASTA and GFF from reference.
[07:02:29] Wrote 1 sequences to ref.fa
[07:02:29] Wrote 0 features to ref.gff
[07:02:29] Shredding /corral4/main/objects/3/9/7/dataset_3976135c-0036-4694-8aea-44389097c194.dat into pseudo-reads
[07:02:31] Wrote 219558 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:02:31] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[07:02:31] Using BAM RG (Read Group) ID: BVBRC_genome_sequence__83__fasta
[07:02:31] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:02:31] Running: bwa index reference/ref.fa 2>> snps.log
[07:02:32] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[07:02:32] Running: ln -sf reference/ref.fa . 2>> snps.log
[07:02:32] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[07:02:32] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[07:02:32] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence__83__fasta\tSM:BVBRC_genome_sequence__83__fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261288/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261288/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261288/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[s |
| 1 | [07:05:17] This is snippy 4.6.0Show full stderr[07:05:17] This is snippy 4.6.0
[07:05:17] Written by Torsten Seemann
[07:05:17] Obtained from https://github.com/tseemann/snippy
[07:05:17] Detected operating system: linux
[07:05:17] Enabling bundled linux tools.
[07:05:17] Found bwa - /usr/local/bin/bwa
[07:05:17] Found bcftools - /usr/local/bin/bcftools
[07:05:17] Found samtools - /usr/local/bin/samtools
[07:05:17] Found java - /usr/local/bin/java
[07:05:17] Found snpEff - /usr/local/bin/snpEff
[07:05:17] Found samclip - /usr/local/bin/samclip
[07:05:17] Found seqtk - /usr/local/bin/seqtk
[07:05:17] Found parallel - /usr/local/bin/parallel
[07:05:17] Found freebayes - /usr/local/bin/freebayes
[07:05:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:17] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:17] Found gzip - /bin/gzip
[07:05:17] Found vt - /usr/local/bin/vt
[07:05:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:18] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:05:18] Treating reference as 'fasta' format.
[07:05:18] Will use 1 CPU cores.
[07:05:18] Using read file: /corral4/main/objects/2/f/9/dataset_2f99f301-ceb0-46ae-9329-f84db170cf49.dat
[07:05:18] Creating folder: BVBRC_genome_sequence___2025_10_25T135706_786_fasta
[07:05:18] Changing working directory: BVBRC_genome_sequence___2025_10_25T135706_786_fasta
[07:05:18] Creating reference folder: reference
[07:05:18] Extracting FASTA and GFF from reference.
[07:05:18] Wrote 1 sequences to ref.fa
[07:05:18] Wrote 0 features to ref.gff
[07:05:18] Shredding /corral4/main/objects/2/f/9/dataset_2f99f301-ceb0-46ae-9329-f84db170cf49.dat into pseudo-reads
[07:05:20] Wrote 236178 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:05:20] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[07:05:20] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135706_786_fasta
[07:05:20] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:05:20] Running: bwa index reference/ref.fa 2>> snps.log
[07:05:22] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[07:05:22] Running: ln -sf reference/ref.fa . 2>> snps.log
[07:05:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[07:05:22] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[07:05:22] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135706_786_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135706_786_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261363/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261363/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261363/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samcl |
| 1 | [07:05:35] This is snippy 4.6.0Show full stderr[07:05:35] This is snippy 4.6.0
[07:05:35] Written by Torsten Seemann
[07:05:35] Obtained from https://github.com/tseemann/snippy
[07:05:35] Detected operating system: linux
[07:05:35] Enabling bundled linux tools.
[07:05:35] Found bwa - /usr/local/bin/bwa
[07:05:35] Found bcftools - /usr/local/bin/bcftools
[07:05:35] Found samtools - /usr/local/bin/samtools
[07:05:35] Found java - /usr/local/bin/java
[07:05:35] Found snpEff - /usr/local/bin/snpEff
[07:05:35] Found samclip - /usr/local/bin/samclip
[07:05:35] Found seqtk - /usr/local/bin/seqtk
[07:05:35] Found parallel - /usr/local/bin/parallel
[07:05:35] Found freebayes - /usr/local/bin/freebayes
[07:05:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:35] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:35] Found gzip - /bin/gzip
[07:05:35] Found vt - /usr/local/bin/vt
[07:05:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:36] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat
[07:05:36] Treating reference as 'fasta' format.
[07:05:36] Will use 1 CPU cores.
[07:05:36] Using read file: /corral4/main/objects/b/0/9/dataset_b09d551a-c85b-4b80-9753-ef6046602025.dat
[07:05:36] Creating folder: BVBRC_genome_sequence__11__fasta
[07:05:36] Changing working directory: BVBRC_genome_sequence__11__fasta
[07:05:36] Creating reference folder: reference
[07:05:36] Extracting FASTA and GFF from reference.
[07:05:36] Wrote 1 sequences to ref.fa
[07:05:36] Wrote 0 features to ref.gff
[07:05:36] Shredding /corral4/main/objects/b/0/9/dataset_b09d551a-c85b-4b80-9753-ef6046602025.dat into pseudo-reads
[07:05:38] Wrote 221348 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[07:05:38] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time.
[07:05:38] Using BAM RG (Read Group) ID: BVBRC_genome_sequence__11__fasta
[07:05:38] Running: samtools faidx reference/ref.fa 2>> snps.log
[07:05:38] Running: bwa index reference/ref.fa 2>> snps.log
[07:05:39] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[07:05:40] Running: ln -sf reference/ref.fa . 2>> snps.log
[07:05:40] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[07:05:40] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[07:05:40] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence__11__fasta\tSM:BVBRC_genome_sequence__11__fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261397/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261397/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261397/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[s |
| 1 | [06:48:17] This is snippy 4.6.0Show full stderr[06:48:17] This is snippy 4.6.0
[06:48:17] Written by Torsten Seemann
[06:48:17] Obtained from https://github.com/tseemann/snippy
[06:48:17] Detected operating system: linux
[06:48:17] Enabling bundled linux tools.
[06:48:17] Found bwa - /usr/local/bin/bwa
[06:48:17] Found bcftools - /usr/local/bin/bcftools
[06:48:17] Found samtools - /usr/local/bin/samtools
[06:48:17] Found java - /usr/local/bin/java
[06:48:17] Found snpEff - /usr/local/bin/snpEff
[06:48:17] Found samclip - /usr/local/bin/samclip
[06:48:17] Found seqtk - /usr/local/bin/seqtk
[06:48:17] Found parallel - /usr/local/bin/parallel
[06:48:17] Found freebayes - /usr/local/bin/freebayes
[06:48:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:17] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:17] Found gzip - /bin/gzip
[06:48:17] Found vt - /usr/local/bin/vt
[06:48:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:49:00] This is snippy 4.6.0Show full stderr[06:49:00] This is snippy 4.6.0
[06:49:00] Written by Torsten Seemann
[06:49:00] Obtained from https://github.com/tseemann/snippy
[06:49:00] Detected operating system: linux
[06:49:00] Enabling bundled linux tools.
[06:49:00] Found bwa - /usr/local/bin/bwa
[06:49:00] Found bcftools - /usr/local/bin/bcftools
[06:49:00] Found samtools - /usr/local/bin/samtools
[06:49:00] Found java - /usr/local/bin/java
[06:49:00] Found snpEff - /usr/local/bin/snpEff
[06:49:00] Found samclip - /usr/local/bin/samclip
[06:49:00] Found seqtk - /usr/local/bin/seqtk
[06:49:00] Found parallel - /usr/local/bin/parallel
[06:49:00] Found freebayes - /usr/local/bin/freebayes
[06:49:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:49:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:49:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:49:00] Found vcfuniq - /usr/local/bin/vcfuniq
[06:49:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:49:00] Found gzip - /bin/gzip
[06:49:00] Found vt - /usr/local/bin/vt
[06:49:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:49:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:49:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:49:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:49:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:49:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:49:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:49:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:00:39] This is snippy 4.6.0Show full stderr[07:00:39] This is snippy 4.6.0
[07:00:39] Written by Torsten Seemann
[07:00:39] Obtained from https://github.com/tseemann/snippy
[07:00:39] Detected operating system: linux
[07:00:39] Enabling bundled linux tools.
[07:00:39] Found bwa - /usr/local/bin/bwa
[07:00:39] Found bcftools - /usr/local/bin/bcftools
[07:00:39] Found samtools - /usr/local/bin/samtools
[07:00:39] Found java - /usr/local/bin/java
[07:00:39] Found snpEff - /usr/local/bin/snpEff
[07:00:39] Found samclip - /usr/local/bin/samclip
[07:00:39] Found seqtk - /usr/local/bin/seqtk
[07:00:39] Found parallel - /usr/local/bin/parallel
[07:00:39] Found freebayes - /usr/local/bin/freebayes
[07:00:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:39] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:39] Found gzip - /bin/gzip
[07:00:39] Found vt - /usr/local/bin/vt
[07:00:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:06:23] This is snippy 4.6.0Show full stderr[07:06:23] This is snippy 4.6.0
[07:06:23] Written by Torsten Seemann
[07:06:23] Obtained from https://github.com/tseemann/snippy
[07:06:23] Detected operating system: linux
[07:06:23] Enabling bundled linux tools.
[07:06:24] Found bwa - /usr/local/bin/bwa
[07:06:24] Found bcftools - /usr/local/bin/bcftools
[07:06:24] Found samtools - /usr/local/bin/samtools
[07:06:24] Found java - /usr/local/bin/java
[07:06:24] Found snpEff - /usr/local/bin/snpEff
[07:06:24] Found samclip - /usr/local/bin/samclip
[07:06:24] Found seqtk - /usr/local/bin/seqtk
[07:06:24] Found parallel - /usr/local/bin/parallel
[07:06:24] Found freebayes - /usr/local/bin/freebayes
[07:06:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:24] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:24] Found gzip - /bin/gzip
[07:06:24] Found vt - /usr/local/bin/vt
[07:06:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:49:33] This is snippy 4.6.0Show full stderr[06:49:33] This is snippy 4.6.0
[06:49:33] Written by Torsten Seemann
[06:49:33] Obtained from https://github.com/tseemann/snippy
[06:49:33] Detected operating system: linux
[06:49:33] Enabling bundled linux tools.
[06:49:33] Found bwa - /usr/local/bin/bwa
[06:49:33] Found bcftools - /usr/local/bin/bcftools
[06:49:33] Found samtools - /usr/local/bin/samtools
[06:49:33] Found java - /usr/local/bin/java
[06:49:33] Found snpEff - /usr/local/bin/snpEff
[06:49:33] Found samclip - /usr/local/bin/samclip
[06:49:33] Found seqtk - /usr/local/bin/seqtk
[06:49:33] Found parallel - /usr/local/bin/parallel
[06:49:33] Found freebayes - /usr/local/bin/freebayes
[06:49:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:49:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:49:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:49:33] Found vcfuniq - /usr/local/bin/vcfuniq
[06:49:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:49:33] Found gzip - /bin/gzip
[06:49:33] Found vt - /usr/local/bin/vt
[06:49:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:49:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:49:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:49:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:49:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:49:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:49:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:49:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:48:13] This is snippy 4.6.0Show full stderr[06:48:13] This is snippy 4.6.0
[06:48:13] Written by Torsten Seemann
[06:48:13] Obtained from https://github.com/tseemann/snippy
[06:48:13] Detected operating system: linux
[06:48:13] Enabling bundled linux tools.
[06:48:13] Found bwa - /usr/local/bin/bwa
[06:48:13] Found bcftools - /usr/local/bin/bcftools
[06:48:13] Found samtools - /usr/local/bin/samtools
[06:48:13] Found java - /usr/local/bin/java
[06:48:13] Found snpEff - /usr/local/bin/snpEff
[06:48:13] Found samclip - /usr/local/bin/samclip
[06:48:13] Found seqtk - /usr/local/bin/seqtk
[06:48:13] Found parallel - /usr/local/bin/parallel
[06:48:13] Found freebayes - /usr/local/bin/freebayes
[06:48:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:13] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:13] Found gzip - /bin/gzip
[06:48:13] Found vt - /usr/local/bin/vt
[06:48:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:54:26] This is snippy 4.6.0Show full stderr[06:54:26] This is snippy 4.6.0
[06:54:26] Written by Torsten Seemann
[06:54:26] Obtained from https://github.com/tseemann/snippy
[06:54:26] Detected operating system: linux
[06:54:26] Enabling bundled linux tools.
[06:54:26] Found bwa - /usr/local/bin/bwa
[06:54:26] Found bcftools - /usr/local/bin/bcftools
[06:54:26] Found samtools - /usr/local/bin/samtools
[06:54:26] Found java - /usr/local/bin/java
[06:54:26] Found snpEff - /usr/local/bin/snpEff
[06:54:26] Found samclip - /usr/local/bin/samclip
[06:54:26] Found seqtk - /usr/local/bin/seqtk
[06:54:26] Found parallel - /usr/local/bin/parallel
[06:54:26] Found freebayes - /usr/local/bin/freebayes
[06:54:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:26] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:26] Found gzip - /bin/gzip
[06:54:26] Found vt - /usr/local/bin/vt
[06:54:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:06:53] This is snippy 4.6.0Show full stderr[07:06:53] This is snippy 4.6.0
[07:06:53] Written by Torsten Seemann
[07:06:53] Obtained from https://github.com/tseemann/snippy
[07:06:53] Detected operating system: linux
[07:06:53] Enabling bundled linux tools.
[07:06:53] Found bwa - /usr/local/bin/bwa
[07:06:53] Found bcftools - /usr/local/bin/bcftools
[07:06:53] Found samtools - /usr/local/bin/samtools
[07:06:53] Found java - /usr/local/bin/java
[07:06:53] Found snpEff - /usr/local/bin/snpEff
[07:06:53] Found samclip - /usr/local/bin/samclip
[07:06:53] Found seqtk - /usr/local/bin/seqtk
[07:06:53] Found parallel - /usr/local/bin/parallel
[07:06:53] Found freebayes - /usr/local/bin/freebayes
[07:06:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:53] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:53] Found gzip - /bin/gzip
[07:06:53] Found vt - /usr/local/bin/vt
[07:06:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:09] This is snippy 4.6.0Show full stderr[07:07:09] This is snippy 4.6.0
[07:07:09] Written by Torsten Seemann
[07:07:09] Obtained from https://github.com/tseemann/snippy
[07:07:09] Detected operating system: linux
[07:07:09] Enabling bundled linux tools.
[07:07:09] Found bwa - /usr/local/bin/bwa
[07:07:09] Found bcftools - /usr/local/bin/bcftools
[07:07:09] Found samtools - /usr/local/bin/samtools
[07:07:09] Found java - /usr/local/bin/java
[07:07:09] Found snpEff - /usr/local/bin/snpEff
[07:07:09] Found samclip - /usr/local/bin/samclip
[07:07:09] Found seqtk - /usr/local/bin/seqtk
[07:07:09] Found parallel - /usr/local/bin/parallel
[07:07:09] Found freebayes - /usr/local/bin/freebayes
[07:07:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:09] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:09] Found gzip - /bin/gzip
[07:07:09] Found vt - /usr/local/bin/vt
[07:07:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:48:09] This is snippy 4.6.0Show full stderr[06:48:09] This is snippy 4.6.0
[06:48:09] Written by Torsten Seemann
[06:48:09] Obtained from https://github.com/tseemann/snippy
[06:48:09] Detected operating system: linux
[06:48:09] Enabling bundled linux tools.
[06:48:09] Found bwa - /usr/local/bin/bwa
[06:48:09] Found bcftools - /usr/local/bin/bcftools
[06:48:09] Found samtools - /usr/local/bin/samtools
[06:48:09] Found java - /usr/local/bin/java
[06:48:09] Found snpEff - /usr/local/bin/snpEff
[06:48:09] Found samclip - /usr/local/bin/samclip
[06:48:10] Found seqtk - /usr/local/bin/seqtk
[06:48:10] Found parallel - /usr/local/bin/parallel
[06:48:10] Found freebayes - /usr/local/bin/freebayes
[06:48:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:10] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:10] Found gzip - /bin/gzip
[06:48:10] Found vt - /usr/local/bin/vt
[06:48:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:48:54] This is snippy 4.6.0Show full stderr[06:48:54] This is snippy 4.6.0
[06:48:54] Written by Torsten Seemann
[06:48:54] Obtained from https://github.com/tseemann/snippy
[06:48:54] Detected operating system: linux
[06:48:54] Enabling bundled linux tools.
[06:48:54] Found bwa - /usr/local/bin/bwa
[06:48:54] Found bcftools - /usr/local/bin/bcftools
[06:48:54] Found samtools - /usr/local/bin/samtools
[06:48:54] Found java - /usr/local/bin/java
[06:48:54] Found snpEff - /usr/local/bin/snpEff
[06:48:54] Found samclip - /usr/local/bin/samclip
[06:48:54] Found seqtk - /usr/local/bin/seqtk
[06:48:54] Found parallel - /usr/local/bin/parallel
[06:48:54] Found freebayes - /usr/local/bin/freebayes
[06:48:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:54] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:54] Found gzip - /bin/gzip
[06:48:54] Found vt - /usr/local/bin/vt
[06:48:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:48:57] This is snippy 4.6.0Show full stderr[06:48:57] This is snippy 4.6.0
[06:48:57] Written by Torsten Seemann
[06:48:57] Obtained from https://github.com/tseemann/snippy
[06:48:57] Detected operating system: linux
[06:48:57] Enabling bundled linux tools.
[06:48:57] Found bwa - /usr/local/bin/bwa
[06:48:57] Found bcftools - /usr/local/bin/bcftools
[06:48:57] Found samtools - /usr/local/bin/samtools
[06:48:57] Found java - /usr/local/bin/java
[06:48:57] Found snpEff - /usr/local/bin/snpEff
[06:48:57] Found samclip - /usr/local/bin/samclip
[06:48:57] Found seqtk - /usr/local/bin/seqtk
[06:48:57] Found parallel - /usr/local/bin/parallel
[06:48:57] Found freebayes - /usr/local/bin/freebayes
[06:48:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:57] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:57] Found gzip - /bin/gzip
[06:48:57] Found vt - /usr/local/bin/vt
[06:48:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:59:57] This is snippy 4.6.0Show full stderr[06:59:57] This is snippy 4.6.0
[06:59:57] Written by Torsten Seemann
[06:59:57] Obtained from https://github.com/tseemann/snippy
[06:59:57] Detected operating system: linux
[06:59:57] Enabling bundled linux tools.
[06:59:57] Found bwa - /usr/local/bin/bwa
[06:59:57] Found bcftools - /usr/local/bin/bcftools
[06:59:57] Found samtools - /usr/local/bin/samtools
[06:59:57] Found java - /usr/local/bin/java
[06:59:57] Found snpEff - /usr/local/bin/snpEff
[06:59:57] Found samclip - /usr/local/bin/samclip
[06:59:57] Found seqtk - /usr/local/bin/seqtk
[06:59:57] Found parallel - /usr/local/bin/parallel
[06:59:57] Found freebayes - /usr/local/bin/freebayes
[06:59:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:57] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:57] Found gzip - /bin/gzip
[06:59:57] Found vt - /usr/local/bin/vt
[06:59:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:49:25] This is snippy 4.6.0Show full stderr[06:49:25] This is snippy 4.6.0
[06:49:25] Written by Torsten Seemann
[06:49:25] Obtained from https://github.com/tseemann/snippy
[06:49:25] Detected operating system: linux
[06:49:25] Enabling bundled linux tools.
[06:49:25] Found bwa - /usr/local/bin/bwa
[06:49:25] Found bcftools - /usr/local/bin/bcftools
[06:49:25] Found samtools - /usr/local/bin/samtools
[06:49:25] Found java - /usr/local/bin/java
[06:49:25] Found snpEff - /usr/local/bin/snpEff
[06:49:25] Found samclip - /usr/local/bin/samclip
[06:49:25] Found seqtk - /usr/local/bin/seqtk
[06:49:25] Found parallel - /usr/local/bin/parallel
[06:49:25] Found freebayes - /usr/local/bin/freebayes
[06:49:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:49:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:49:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:49:25] Found vcfuniq - /usr/local/bin/vcfuniq
[06:49:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:49:25] Found gzip - /bin/gzip
[06:49:25] Found vt - /usr/local/bin/vt
[06:49:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:49:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:49:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:49:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:49:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:49:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:49:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:49:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:10] This is snippy 4.6.0Show full stderr[07:07:10] This is snippy 4.6.0
[07:07:10] Written by Torsten Seemann
[07:07:10] Obtained from https://github.com/tseemann/snippy
[07:07:10] Detected operating system: linux
[07:07:10] Enabling bundled linux tools.
[07:07:10] Found bwa - /usr/local/bin/bwa
[07:07:10] Found bcftools - /usr/local/bin/bcftools
[07:07:10] Found samtools - /usr/local/bin/samtools
[07:07:10] Found java - /usr/local/bin/java
[07:07:10] Found snpEff - /usr/local/bin/snpEff
[07:07:10] Found samclip - /usr/local/bin/samclip
[07:07:10] Found seqtk - /usr/local/bin/seqtk
[07:07:10] Found parallel - /usr/local/bin/parallel
[07:07:10] Found freebayes - /usr/local/bin/freebayes
[07:07:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:10] Found gzip - /bin/gzip
[07:07:10] Found vt - /usr/local/bin/vt
[07:07:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:53:56] This is snippy 4.6.0Show full stderr[06:53:56] This is snippy 4.6.0
[06:53:56] Written by Torsten Seemann
[06:53:56] Obtained from https://github.com/tseemann/snippy
[06:53:56] Detected operating system: linux
[06:53:56] Enabling bundled linux tools.
[06:53:56] Found bwa - /usr/local/bin/bwa
[06:53:56] Found bcftools - /usr/local/bin/bcftools
[06:53:56] Found samtools - /usr/local/bin/samtools
[06:53:56] Found java - /usr/local/bin/java
[06:53:56] Found snpEff - /usr/local/bin/snpEff
[06:53:56] Found samclip - /usr/local/bin/samclip
[06:53:56] Found seqtk - /usr/local/bin/seqtk
[06:53:56] Found parallel - /usr/local/bin/parallel
[06:53:56] Found freebayes - /usr/local/bin/freebayes
[06:53:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:56] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:56] Found gzip - /bin/gzip
[06:53:56] Found vt - /usr/local/bin/vt
[06:53:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:54:09] This is snippy 4.6.0Show full stderr[06:54:09] This is snippy 4.6.0
[06:54:09] Written by Torsten Seemann
[06:54:09] Obtained from https://github.com/tseemann/snippy
[06:54:09] Detected operating system: linux
[06:54:09] Enabling bundled linux tools.
[06:54:09] Found bwa - /usr/local/bin/bwa
[06:54:09] Found bcftools - /usr/local/bin/bcftools
[06:54:09] Found samtools - /usr/local/bin/samtools
[06:54:09] Found java - /usr/local/bin/java
[06:54:09] Found snpEff - /usr/local/bin/snpEff
[06:54:09] Found samclip - /usr/local/bin/samclip
[06:54:09] Found seqtk - /usr/local/bin/seqtk
[06:54:09] Found parallel - /usr/local/bin/parallel
[06:54:09] Found freebayes - /usr/local/bin/freebayes
[06:54:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:09] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:09] Found gzip - /bin/gzip
[06:54:09] Found vt - /usr/local/bin/vt
[06:54:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:54:06] This is snippy 4.6.0Show full stderr[06:54:06] This is snippy 4.6.0
[06:54:06] Written by Torsten Seemann
[06:54:06] Obtained from https://github.com/tseemann/snippy
[06:54:06] Detected operating system: linux
[06:54:06] Enabling bundled linux tools.
[06:54:06] Found bwa - /usr/local/bin/bwa
[06:54:06] Found bcftools - /usr/local/bin/bcftools
[06:54:06] Found samtools - /usr/local/bin/samtools
[06:54:06] Found java - /usr/local/bin/java
[06:54:06] Found snpEff - /usr/local/bin/snpEff
[06:54:06] Found samclip - /usr/local/bin/samclip
[06:54:06] Found seqtk - /usr/local/bin/seqtk
[06:54:06] Found parallel - /usr/local/bin/parallel
[06:54:06] Found freebayes - /usr/local/bin/freebayes
[06:54:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:06] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:06] Found gzip - /bin/gzip
[06:54:06] Found vt - /usr/local/bin/vt
[06:54:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:48:44] This is snippy 4.6.0Show full stderr[06:48:44] This is snippy 4.6.0
[06:48:44] Written by Torsten Seemann
[06:48:44] Obtained from https://github.com/tseemann/snippy
[06:48:44] Detected operating system: linux
[06:48:44] Enabling bundled linux tools.
[06:48:44] Found bwa - /usr/local/bin/bwa
[06:48:44] Found bcftools - /usr/local/bin/bcftools
[06:48:44] Found samtools - /usr/local/bin/samtools
[06:48:44] Found java - /usr/local/bin/java
[06:48:44] Found snpEff - /usr/local/bin/snpEff
[06:48:44] Found samclip - /usr/local/bin/samclip
[06:48:44] Found seqtk - /usr/local/bin/seqtk
[06:48:44] Found parallel - /usr/local/bin/parallel
[06:48:44] Found freebayes - /usr/local/bin/freebayes
[06:48:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:44] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:44] Found gzip - /bin/gzip
[06:48:44] Found vt - /usr/local/bin/vt
[06:48:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:12:20] This is snippy 4.6.0Show full stderr[07:12:20] This is snippy 4.6.0
[07:12:20] Written by Torsten Seemann
[07:12:20] Obtained from https://github.com/tseemann/snippy
[07:12:20] Detected operating system: linux
[07:12:20] Enabling bundled linux tools.
[07:12:20] Found bwa - /usr/local/bin/bwa
[07:12:20] Found bcftools - /usr/local/bin/bcftools
[07:12:20] Found samtools - /usr/local/bin/samtools
[07:12:20] Found java - /usr/local/bin/java
[07:12:20] Found snpEff - /usr/local/bin/snpEff
[07:12:20] Found samclip - /usr/local/bin/samclip
[07:12:20] Found seqtk - /usr/local/bin/seqtk
[07:12:20] Found parallel - /usr/local/bin/parallel
[07:12:20] Found freebayes - /usr/local/bin/freebayes
[07:12:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:12:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:12:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:12:20] Found vcfuniq - /usr/local/bin/vcfuniq
[07:12:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:12:20] Found gzip - /bin/gzip
[07:12:20] Found vt - /usr/local/bin/vt
[07:12:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:12:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:12:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:12:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:12:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:12:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:12:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:12:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:12:44] This is snippy 4.6.0Show full stderr[07:12:44] This is snippy 4.6.0
[07:12:44] Written by Torsten Seemann
[07:12:44] Obtained from https://github.com/tseemann/snippy
[07:12:44] Detected operating system: linux
[07:12:44] Enabling bundled linux tools.
[07:12:44] Found bwa - /usr/local/bin/bwa
[07:12:44] Found bcftools - /usr/local/bin/bcftools
[07:12:44] Found samtools - /usr/local/bin/samtools
[07:12:44] Found java - /usr/local/bin/java
[07:12:44] Found snpEff - /usr/local/bin/snpEff
[07:12:44] Found samclip - /usr/local/bin/samclip
[07:12:44] Found seqtk - /usr/local/bin/seqtk
[07:12:44] Found parallel - /usr/local/bin/parallel
[07:12:44] Found freebayes - /usr/local/bin/freebayes
[07:12:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:12:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:12:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:12:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:12:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:12:44] Found gzip - /bin/gzip
[07:12:44] Found vt - /usr/local/bin/vt
[07:12:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:12:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:12:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:12:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:12:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:12:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:12:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:12:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:19:00] This is snippy 4.6.0Show full stderr[07:19:00] This is snippy 4.6.0
[07:19:00] Written by Torsten Seemann
[07:19:00] Obtained from https://github.com/tseemann/snippy
[07:19:00] Detected operating system: linux
[07:19:00] Enabling bundled linux tools.
[07:19:00] Found bwa - /usr/local/bin/bwa
[07:19:00] Found bcftools - /usr/local/bin/bcftools
[07:19:00] Found samtools - /usr/local/bin/samtools
[07:19:00] Found java - /usr/local/bin/java
[07:19:00] Found snpEff - /usr/local/bin/snpEff
[07:19:00] Found samclip - /usr/local/bin/samclip
[07:19:00] Found seqtk - /usr/local/bin/seqtk
[07:19:00] Found parallel - /usr/local/bin/parallel
[07:19:00] Found freebayes - /usr/local/bin/freebayes
[07:19:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:19:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:19:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:19:00] Found vcfuniq - /usr/local/bin/vcfuniq
[07:19:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:19:00] Found gzip - /bin/gzip
[07:19:00] Found vt - /usr/local/bin/vt
[07:19:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:19:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:19:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:19:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:19:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:19:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:19:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:19:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:19:44] This is snippy 4.6.0Show full stderr[07:19:44] This is snippy 4.6.0
[07:19:44] Written by Torsten Seemann
[07:19:44] Obtained from https://github.com/tseemann/snippy
[07:19:44] Detected operating system: linux
[07:19:44] Enabling bundled linux tools.
[07:19:44] Found bwa - /usr/local/bin/bwa
[07:19:44] Found bcftools - /usr/local/bin/bcftools
[07:19:44] Found samtools - /usr/local/bin/samtools
[07:19:44] Found java - /usr/local/bin/java
[07:19:44] Found snpEff - /usr/local/bin/snpEff
[07:19:44] Found samclip - /usr/local/bin/samclip
[07:19:44] Found seqtk - /usr/local/bin/seqtk
[07:19:44] Found parallel - /usr/local/bin/parallel
[07:19:44] Found freebayes - /usr/local/bin/freebayes
[07:19:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:19:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:19:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:19:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:19:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:19:44] Found gzip - /bin/gzip
[07:19:44] Found vt - /usr/local/bin/vt
[07:19:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:19:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:19:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:19:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:19:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:19:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:19:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:19:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:49:39] This is snippy 4.6.0Show full stderr[06:49:39] This is snippy 4.6.0
[06:49:39] Written by Torsten Seemann
[06:49:39] Obtained from https://github.com/tseemann/snippy
[06:49:39] Detected operating system: linux
[06:49:39] Enabling bundled linux tools.
[06:49:39] Found bwa - /usr/local/bin/bwa
[06:49:39] Found bcftools - /usr/local/bin/bcftools
[06:49:39] Found samtools - /usr/local/bin/samtools
[06:49:39] Found java - /usr/local/bin/java
[06:49:39] Found snpEff - /usr/local/bin/snpEff
[06:49:39] Found samclip - /usr/local/bin/samclip
[06:49:39] Found seqtk - /usr/local/bin/seqtk
[06:49:39] Found parallel - /usr/local/bin/parallel
[06:49:39] Found freebayes - /usr/local/bin/freebayes
[06:49:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:49:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:49:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:49:39] Found vcfuniq - /usr/local/bin/vcfuniq
[06:49:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:49:39] Found gzip - /bin/gzip
[06:49:39] Found vt - /usr/local/bin/vt
[06:49:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:49:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:49:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:49:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:49:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:49:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:49:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:49:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:26:47] This is snippy 4.6.0Show full stderr[07:26:47] This is snippy 4.6.0
[07:26:47] Written by Torsten Seemann
[07:26:47] Obtained from https://github.com/tseemann/snippy
[07:26:47] Detected operating system: linux
[07:26:47] Enabling bundled linux tools.
[07:26:47] Found bwa - /usr/local/bin/bwa
[07:26:47] Found bcftools - /usr/local/bin/bcftools
[07:26:47] Found samtools - /usr/local/bin/samtools
[07:26:47] Found java - /usr/local/bin/java
[07:26:47] Found snpEff - /usr/local/bin/snpEff
[07:26:47] Found samclip - /usr/local/bin/samclip
[07:26:47] Found seqtk - /usr/local/bin/seqtk
[07:26:47] Found parallel - /usr/local/bin/parallel
[07:26:47] Found freebayes - /usr/local/bin/freebayes
[07:26:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:26:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:26:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:26:48] Found vcfuniq - /usr/local/bin/vcfuniq
[07:26:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:26:48] Found gzip - /bin/gzip
[07:26:48] Found vt - /usr/local/bin/vt
[07:26:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:26:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:26:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:26:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:26:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:26:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:26:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:26:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:31:56] This is snippy 4.6.0Show full stderr[07:31:56] This is snippy 4.6.0
[07:31:56] Written by Torsten Seemann
[07:31:56] Obtained from https://github.com/tseemann/snippy
[07:31:56] Detected operating system: linux
[07:31:56] Enabling bundled linux tools.
[07:31:56] Found bwa - /usr/local/bin/bwa
[07:31:56] Found bcftools - /usr/local/bin/bcftools
[07:31:56] Found samtools - /usr/local/bin/samtools
[07:31:56] Found java - /usr/local/bin/java
[07:31:56] Found snpEff - /usr/local/bin/snpEff
[07:31:56] Found samclip - /usr/local/bin/samclip
[07:31:56] Found seqtk - /usr/local/bin/seqtk
[07:31:56] Found parallel - /usr/local/bin/parallel
[07:31:56] Found freebayes - /usr/local/bin/freebayes
[07:31:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:31:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:31:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:31:56] Found vcfuniq - /usr/local/bin/vcfuniq
[07:31:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:31:56] Found gzip - /bin/gzip
[07:31:56] Found vt - /usr/local/bin/vt
[07:31:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:31:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:31:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:31:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:31:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:31:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:31:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:31:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:48:30] This is snippy 4.6.0Show full stderr[06:48:30] This is snippy 4.6.0
[06:48:30] Written by Torsten Seemann
[06:48:30] Obtained from https://github.com/tseemann/snippy
[06:48:30] Detected operating system: linux
[06:48:30] Enabling bundled linux tools.
[06:48:30] Found bwa - /usr/local/bin/bwa
[06:48:30] Found bcftools - /usr/local/bin/bcftools
[06:48:30] Found samtools - /usr/local/bin/samtools
[06:48:30] Found java - /usr/local/bin/java
[06:48:30] Found snpEff - /usr/local/bin/snpEff
[06:48:30] Found samclip - /usr/local/bin/samclip
[06:48:30] Found seqtk - /usr/local/bin/seqtk
[06:48:30] Found parallel - /usr/local/bin/parallel
[06:48:30] Found freebayes - /usr/local/bin/freebayes
[06:48:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:30] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:30] Found gzip - /bin/gzip
[06:48:30] Found vt - /usr/local/bin/vt
[06:48:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:19:26] This is snippy 4.6.0Show full stderr[07:19:26] This is snippy 4.6.0
[07:19:26] Written by Torsten Seemann
[07:19:26] Obtained from https://github.com/tseemann/snippy
[07:19:26] Detected operating system: linux
[07:19:26] Enabling bundled linux tools.
[07:19:26] Found bwa - /usr/local/bin/bwa
[07:19:26] Found bcftools - /usr/local/bin/bcftools
[07:19:26] Found samtools - /usr/local/bin/samtools
[07:19:26] Found java - /usr/local/bin/java
[07:19:26] Found snpEff - /usr/local/bin/snpEff
[07:19:26] Found samclip - /usr/local/bin/samclip
[07:19:26] Found seqtk - /usr/local/bin/seqtk
[07:19:26] Found parallel - /usr/local/bin/parallel
[07:19:26] Found freebayes - /usr/local/bin/freebayes
[07:19:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:19:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:19:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:19:26] Found vcfuniq - /usr/local/bin/vcfuniq
[07:19:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:19:26] Found gzip - /bin/gzip
[07:19:26] Found vt - /usr/local/bin/vt
[07:19:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:19:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:19:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:19:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:19:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:19:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:19:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:19:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:48:42] This is snippy 4.6.0Show full stderr[06:48:42] This is snippy 4.6.0
[06:48:42] Written by Torsten Seemann
[06:48:42] Obtained from https://github.com/tseemann/snippy
[06:48:42] Detected operating system: linux
[06:48:42] Enabling bundled linux tools.
[06:48:42] Found bwa - /usr/local/bin/bwa
[06:48:42] Found bcftools - /usr/local/bin/bcftools
[06:48:42] Found samtools - /usr/local/bin/samtools
[06:48:42] Found java - /usr/local/bin/java
[06:48:42] Found snpEff - /usr/local/bin/snpEff
[06:48:42] Found samclip - /usr/local/bin/samclip
[06:48:42] Found seqtk - /usr/local/bin/seqtk
[06:48:42] Found parallel - /usr/local/bin/parallel
[06:48:42] Found freebayes - /usr/local/bin/freebayes
[06:48:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:42] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:42] Found gzip - /bin/gzip
[06:48:42] Found vt - /usr/local/bin/vt
[06:48:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:48:51] This is snippy 4.6.0Show full stderr[06:48:51] This is snippy 4.6.0
[06:48:51] Written by Torsten Seemann
[06:48:51] Obtained from https://github.com/tseemann/snippy
[06:48:51] Detected operating system: linux
[06:48:51] Enabling bundled linux tools.
[06:48:51] Found bwa - /usr/local/bin/bwa
[06:48:51] Found bcftools - /usr/local/bin/bcftools
[06:48:51] Found samtools - /usr/local/bin/samtools
[06:48:51] Found java - /usr/local/bin/java
[06:48:51] Found snpEff - /usr/local/bin/snpEff
[06:48:51] Found samclip - /usr/local/bin/samclip
[06:48:51] Found seqtk - /usr/local/bin/seqtk
[06:48:51] Found parallel - /usr/local/bin/parallel
[06:48:51] Found freebayes - /usr/local/bin/freebayes
[06:48:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:48:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:48:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:48:51] Found vcfuniq - /usr/local/bin/vcfuniq
[06:48:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:48:51] Found gzip - /bin/gzip
[06:48:51] Found vt - /usr/local/bin/vt
[06:48:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:48:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:48:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:48:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:48:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:48:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:48:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:48:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:32:11] This is snippy 4.6.0Show full stderr[07:32:11] This is snippy 4.6.0
[07:32:11] Written by Torsten Seemann
[07:32:11] Obtained from https://github.com/tseemann/snippy
[07:32:11] Detected operating system: linux
[07:32:11] Enabling bundled linux tools.
[07:32:11] Found bwa - /usr/local/bin/bwa
[07:32:11] Found bcftools - /usr/local/bin/bcftools
[07:32:11] Found samtools - /usr/local/bin/samtools
[07:32:11] Found java - /usr/local/bin/java
[07:32:11] Found snpEff - /usr/local/bin/snpEff
[07:32:11] Found samclip - /usr/local/bin/samclip
[07:32:11] Found seqtk - /usr/local/bin/seqtk
[07:32:11] Found parallel - /usr/local/bin/parallel
[07:32:11] Found freebayes - /usr/local/bin/freebayes
[07:32:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:11] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:11] Found gzip - /bin/gzip
[07:32:11] Found vt - /usr/local/bin/vt
[07:32:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:32:58] This is snippy 4.6.0Show full stderr[07:32:58] This is snippy 4.6.0
[07:32:58] Written by Torsten Seemann
[07:32:58] Obtained from https://github.com/tseemann/snippy
[07:32:58] Detected operating system: linux
[07:32:58] Enabling bundled linux tools.
[07:32:58] Found bwa - /usr/local/bin/bwa
[07:32:58] Found bcftools - /usr/local/bin/bcftools
[07:32:58] Found samtools - /usr/local/bin/samtools
[07:32:58] Found java - /usr/local/bin/java
[07:32:58] Found snpEff - /usr/local/bin/snpEff
[07:32:58] Found samclip - /usr/local/bin/samclip
[07:32:58] Found seqtk - /usr/local/bin/seqtk
[07:32:58] Found parallel - /usr/local/bin/parallel
[07:32:58] Found freebayes - /usr/local/bin/freebayes
[07:32:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:58] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:58] Found gzip - /bin/gzip
[07:32:58] Found vt - /usr/local/bin/vt
[07:32:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:49:19] This is snippy 4.6.0Show full stderr[06:49:19] This is snippy 4.6.0
[06:49:19] Written by Torsten Seemann
[06:49:19] Obtained from https://github.com/tseemann/snippy
[06:49:19] Detected operating system: linux
[06:49:19] Enabling bundled linux tools.
[06:49:19] Found bwa - /usr/local/bin/bwa
[06:49:19] Found bcftools - /usr/local/bin/bcftools
[06:49:19] Found samtools - /usr/local/bin/samtools
[06:49:19] Found java - /usr/local/bin/java
[06:49:19] Found snpEff - /usr/local/bin/snpEff
[06:49:19] Found samclip - /usr/local/bin/samclip
[06:49:19] Found seqtk - /usr/local/bin/seqtk
[06:49:19] Found parallel - /usr/local/bin/parallel
[06:49:19] Found freebayes - /usr/local/bin/freebayes
[06:49:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:49:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:49:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:49:19] Found vcfuniq - /usr/local/bin/vcfuniq
[06:49:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:49:19] Found gzip - /bin/gzip
[06:49:19] Found vt - /usr/local/bin/vt
[06:49:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:49:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:49:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:49:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:49:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:49:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:49:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:49:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:38:29] This is snippy 4.6.0Show full stderr[07:38:29] This is snippy 4.6.0
[07:38:29] Written by Torsten Seemann
[07:38:29] Obtained from https://github.com/tseemann/snippy
[07:38:29] Detected operating system: linux
[07:38:29] Enabling bundled linux tools.
[07:38:29] Found bwa - /usr/local/bin/bwa
[07:38:29] Found bcftools - /usr/local/bin/bcftools
[07:38:29] Found samtools - /usr/local/bin/samtools
[07:38:29] Found java - /usr/local/bin/java
[07:38:29] Found snpEff - /usr/local/bin/snpEff
[07:38:29] Found samclip - /usr/local/bin/samclip
[07:38:29] Found seqtk - /usr/local/bin/seqtk
[07:38:29] Found parallel - /usr/local/bin/parallel
[07:38:29] Found freebayes - /usr/local/bin/freebayes
[07:38:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:29] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:29] Found gzip - /bin/gzip
[07:38:29] Found vt - /usr/local/bin/vt
[07:38:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:50:35] This is snippy 4.6.0Show full stderr[06:50:35] This is snippy 4.6.0
[06:50:35] Written by Torsten Seemann
[06:50:35] Obtained from https://github.com/tseemann/snippy
[06:50:35] Detected operating system: linux
[06:50:35] Enabling bundled linux tools.
[06:50:35] Found bwa - /usr/local/bin/bwa
[06:50:35] Found bcftools - /usr/local/bin/bcftools
[06:50:35] Found samtools - /usr/local/bin/samtools
[06:50:35] Found java - /usr/local/bin/java
[06:50:35] Found snpEff - /usr/local/bin/snpEff
[06:50:35] Found samclip - /usr/local/bin/samclip
[06:50:35] Found seqtk - /usr/local/bin/seqtk
[06:50:35] Found parallel - /usr/local/bin/parallel
[06:50:35] Found freebayes - /usr/local/bin/freebayes
[06:50:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:50:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:50:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:50:35] Found vcfuniq - /usr/local/bin/vcfuniq
[06:50:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:50:35] Found gzip - /bin/gzip
[06:50:35] Found vt - /usr/local/bin/vt
[06:50:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:50:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:50:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:50:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:50:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:50:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:50:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:50:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:02] This is snippy 4.6.0Show full stderr[07:45:02] This is snippy 4.6.0
[07:45:02] Written by Torsten Seemann
[07:45:02] Obtained from https://github.com/tseemann/snippy
[07:45:02] Detected operating system: linux
[07:45:02] Enabling bundled linux tools.
[07:45:02] Found bwa - /usr/local/bin/bwa
[07:45:02] Found bcftools - /usr/local/bin/bcftools
[07:45:03] Found samtools - /usr/local/bin/samtools
[07:45:03] Found java - /usr/local/bin/java
[07:45:03] Found snpEff - /usr/local/bin/snpEff
[07:45:03] Found samclip - /usr/local/bin/samclip
[07:45:03] Found seqtk - /usr/local/bin/seqtk
[07:45:03] Found parallel - /usr/local/bin/parallel
[07:45:03] Found freebayes - /usr/local/bin/freebayes
[07:45:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:03] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:03] Found gzip - /bin/gzip
[07:45:03] Found vt - /usr/local/bin/vt
[07:45:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:50:47] This is snippy 4.6.0Show full stderr[06:50:47] This is snippy 4.6.0
[06:50:47] Written by Torsten Seemann
[06:50:47] Obtained from https://github.com/tseemann/snippy
[06:50:47] Detected operating system: linux
[06:50:47] Enabling bundled linux tools.
[06:50:47] Found bwa - /usr/local/bin/bwa
[06:50:47] Found bcftools - /usr/local/bin/bcftools
[06:50:47] Found samtools - /usr/local/bin/samtools
[06:50:47] Found java - /usr/local/bin/java
[06:50:47] Found snpEff - /usr/local/bin/snpEff
[06:50:47] Found samclip - /usr/local/bin/samclip
[06:50:47] Found seqtk - /usr/local/bin/seqtk
[06:50:47] Found parallel - /usr/local/bin/parallel
[06:50:47] Found freebayes - /usr/local/bin/freebayes
[06:50:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:50:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:50:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:50:47] Found vcfuniq - /usr/local/bin/vcfuniq
[06:50:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:50:47] Found gzip - /bin/gzip
[06:50:47] Found vt - /usr/local/bin/vt
[06:50:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:50:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:50:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:50:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:50:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:50:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:50:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:50:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:50:50] This is snippy 4.6.0Show full stderr[06:50:50] This is snippy 4.6.0
[06:50:50] Written by Torsten Seemann
[06:50:50] Obtained from https://github.com/tseemann/snippy
[06:50:50] Detected operating system: linux
[06:50:50] Enabling bundled linux tools.
[06:50:50] Found bwa - /usr/local/bin/bwa
[06:50:50] Found bcftools - /usr/local/bin/bcftools
[06:50:50] Found samtools - /usr/local/bin/samtools
[06:50:50] Found java - /usr/local/bin/java
[06:50:50] Found snpEff - /usr/local/bin/snpEff
[06:50:50] Found samclip - /usr/local/bin/samclip
[06:50:50] Found seqtk - /usr/local/bin/seqtk
[06:50:50] Found parallel - /usr/local/bin/parallel
[06:50:50] Found freebayes - /usr/local/bin/freebayes
[06:50:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:50:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:50:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:50:50] Found vcfuniq - /usr/local/bin/vcfuniq
[06:50:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:50:50] Found gzip - /bin/gzip
[06:50:50] Found vt - /usr/local/bin/vt
[06:50:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:50:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:50:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:50:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:50:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:50:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:50:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:50:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:50:57] This is snippy 4.6.0Show full stderr[07:50:57] This is snippy 4.6.0
[07:50:57] Written by Torsten Seemann
[07:50:57] Obtained from https://github.com/tseemann/snippy
[07:50:57] Detected operating system: linux
[07:50:57] Enabling bundled linux tools.
[07:50:57] Found bwa - /usr/local/bin/bwa
[07:50:57] Found bcftools - /usr/local/bin/bcftools
[07:50:57] Found samtools - /usr/local/bin/samtools
[07:50:57] Found java - /usr/local/bin/java
[07:50:57] Found snpEff - /usr/local/bin/snpEff
[07:50:57] Found samclip - /usr/local/bin/samclip
[07:50:57] Found seqtk - /usr/local/bin/seqtk
[07:50:57] Found parallel - /usr/local/bin/parallel
[07:50:57] Found freebayes - /usr/local/bin/freebayes
[07:50:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:50:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:50:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:50:57] Found vcfuniq - /usr/local/bin/vcfuniq
[07:50:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:50:58] Found gzip - /bin/gzip
[07:50:58] Found vt - /usr/local/bin/vt
[07:50:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:50:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:50:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:50:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:50:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:50:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:50:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:50:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:57:02] This is snippy 4.6.0Show full stderr[07:57:02] This is snippy 4.6.0
[07:57:02] Written by Torsten Seemann
[07:57:02] Obtained from https://github.com/tseemann/snippy
[07:57:02] Detected operating system: linux
[07:57:02] Enabling bundled linux tools.
[07:57:02] Found bwa - /usr/local/bin/bwa
[07:57:02] Found bcftools - /usr/local/bin/bcftools
[07:57:02] Found samtools - /usr/local/bin/samtools
[07:57:02] Found java - /usr/local/bin/java
[07:57:02] Found snpEff - /usr/local/bin/snpEff
[07:57:02] Found samclip - /usr/local/bin/samclip
[07:57:02] Found seqtk - /usr/local/bin/seqtk
[07:57:02] Found parallel - /usr/local/bin/parallel
[07:57:02] Found freebayes - /usr/local/bin/freebayes
[07:57:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:57:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:57:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:57:02] Found vcfuniq - /usr/local/bin/vcfuniq
[07:57:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:57:02] Found gzip - /bin/gzip
[07:57:02] Found vt - /usr/local/bin/vt
[07:57:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:57:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:57:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:57:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:57:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:57:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:57:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:57:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:57:04] This is snippy 4.6.0Show full stderr[07:57:04] This is snippy 4.6.0
[07:57:04] Written by Torsten Seemann
[07:57:04] Obtained from https://github.com/tseemann/snippy
[07:57:04] Detected operating system: linux
[07:57:04] Enabling bundled linux tools.
[07:57:04] Found bwa - /usr/local/bin/bwa
[07:57:04] Found bcftools - /usr/local/bin/bcftools
[07:57:04] Found samtools - /usr/local/bin/samtools
[07:57:04] Found java - /usr/local/bin/java
[07:57:04] Found snpEff - /usr/local/bin/snpEff
[07:57:04] Found samclip - /usr/local/bin/samclip
[07:57:04] Found seqtk - /usr/local/bin/seqtk
[07:57:04] Found parallel - /usr/local/bin/parallel
[07:57:04] Found freebayes - /usr/local/bin/freebayes
[07:57:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:57:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:57:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:57:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:57:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:57:04] Found gzip - /bin/gzip
[07:57:04] Found vt - /usr/local/bin/vt
[07:57:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:57:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:57:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:57:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:57:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:57:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:57:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:57:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:12:56] This is snippy 4.6.0Show full stderr[07:12:56] This is snippy 4.6.0
[07:12:56] Written by Torsten Seemann
[07:12:56] Obtained from https://github.com/tseemann/snippy
[07:12:56] Detected operating system: linux
[07:12:56] Enabling bundled linux tools.
[07:12:56] Found bwa - /usr/local/bin/bwa
[07:12:56] Found bcftools - /usr/local/bin/bcftools
[07:12:56] Found samtools - /usr/local/bin/samtools
[07:12:56] Found java - /usr/local/bin/java
[07:12:56] Found snpEff - /usr/local/bin/snpEff
[07:12:56] Found samclip - /usr/local/bin/samclip
[07:12:56] Found seqtk - /usr/local/bin/seqtk
[07:12:56] Found parallel - /usr/local/bin/parallel
[07:12:56] Found freebayes - /usr/local/bin/freebayes
[07:12:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:12:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:12:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:12:56] Found vcfuniq - /usr/local/bin/vcfuniq
[07:12:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:12:56] Found gzip - /bin/gzip
[07:12:56] Found vt - /usr/local/bin/vt
[07:12:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:12:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:12:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:12:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:12:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:12:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:12:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:12:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:13:32] This is snippy 4.6.0Show full stderr[07:13:32] This is snippy 4.6.0
[07:13:32] Written by Torsten Seemann
[07:13:32] Obtained from https://github.com/tseemann/snippy
[07:13:32] Detected operating system: linux
[07:13:32] Enabling bundled linux tools.
[07:13:32] Found bwa - /usr/local/bin/bwa
[07:13:32] Found bcftools - /usr/local/bin/bcftools
[07:13:32] Found samtools - /usr/local/bin/samtools
[07:13:32] Found java - /usr/local/bin/java
[07:13:32] Found snpEff - /usr/local/bin/snpEff
[07:13:32] Found samclip - /usr/local/bin/samclip
[07:13:32] Found seqtk - /usr/local/bin/seqtk
[07:13:32] Found parallel - /usr/local/bin/parallel
[07:13:32] Found freebayes - /usr/local/bin/freebayes
[07:13:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:13:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:13:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:13:32] Found vcfuniq - /usr/local/bin/vcfuniq
[07:13:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:13:32] Found gzip - /bin/gzip
[07:13:32] Found vt - /usr/local/bin/vt
[07:13:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:13:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:13:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:13:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:13:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:13:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:13:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:13:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:18:50] This is snippy 4.6.0Show full stderr[07:18:50] This is snippy 4.6.0
[07:18:50] Written by Torsten Seemann
[07:18:50] Obtained from https://github.com/tseemann/snippy
[07:18:50] Detected operating system: linux
[07:18:50] Enabling bundled linux tools.
[07:18:50] Found bwa - /usr/local/bin/bwa
[07:18:50] Found bcftools - /usr/local/bin/bcftools
[07:18:50] Found samtools - /usr/local/bin/samtools
[07:18:50] Found java - /usr/local/bin/java
[07:18:50] Found snpEff - /usr/local/bin/snpEff
[07:18:50] Found samclip - /usr/local/bin/samclip
[07:18:50] Found seqtk - /usr/local/bin/seqtk
[07:18:50] Found parallel - /usr/local/bin/parallel
[07:18:50] Found freebayes - /usr/local/bin/freebayes
[07:18:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:18:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:18:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:18:50] Found vcfuniq - /usr/local/bin/vcfuniq
[07:18:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:18:50] Found gzip - /bin/gzip
[07:18:50] Found vt - /usr/local/bin/vt
[07:18:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:18:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:18:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:18:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:18:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:18:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:18:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:18:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:52:14] This is snippy 4.6.0Show full stderr[06:52:14] This is snippy 4.6.0
[06:52:14] Written by Torsten Seemann
[06:52:14] Obtained from https://github.com/tseemann/snippy
[06:52:14] Detected operating system: linux
[06:52:14] Enabling bundled linux tools.
[06:52:14] Found bwa - /usr/local/bin/bwa
[06:52:14] Found bcftools - /usr/local/bin/bcftools
[06:52:14] Found samtools - /usr/local/bin/samtools
[06:52:14] Found java - /usr/local/bin/java
[06:52:14] Found snpEff - /usr/local/bin/snpEff
[06:52:14] Found samclip - /usr/local/bin/samclip
[06:52:14] Found seqtk - /usr/local/bin/seqtk
[06:52:14] Found parallel - /usr/local/bin/parallel
[06:52:14] Found freebayes - /usr/local/bin/freebayes
[06:52:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:14] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:14] Found gzip - /bin/gzip
[06:52:14] Found vt - /usr/local/bin/vt
[06:52:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:31] This is snippy 4.6.0Show full stderr[07:45:31] This is snippy 4.6.0
[07:45:31] Written by Torsten Seemann
[07:45:31] Obtained from https://github.com/tseemann/snippy
[07:45:31] Detected operating system: linux
[07:45:31] Enabling bundled linux tools.
[07:45:31] Found bwa - /usr/local/bin/bwa
[07:45:31] Found bcftools - /usr/local/bin/bcftools
[07:45:31] Found samtools - /usr/local/bin/samtools
[07:45:31] Found java - /usr/local/bin/java
[07:45:31] Found snpEff - /usr/local/bin/snpEff
[07:45:31] Found samclip - /usr/local/bin/samclip
[07:45:31] Found seqtk - /usr/local/bin/seqtk
[07:45:31] Found parallel - /usr/local/bin/parallel
[07:45:31] Found freebayes - /usr/local/bin/freebayes
[07:45:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:31] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:31] Found gzip - /bin/gzip
[07:45:31] Found vt - /usr/local/bin/vt
[07:45:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:49:54] This is snippy 4.6.0Show full stderr[06:49:54] This is snippy 4.6.0
[06:49:54] Written by Torsten Seemann
[06:49:54] Obtained from https://github.com/tseemann/snippy
[06:49:54] Detected operating system: linux
[06:49:54] Enabling bundled linux tools.
[06:49:54] Found bwa - /usr/local/bin/bwa
[06:49:54] Found bcftools - /usr/local/bin/bcftools
[06:49:54] Found samtools - /usr/local/bin/samtools
[06:49:54] Found java - /usr/local/bin/java
[06:49:54] Found snpEff - /usr/local/bin/snpEff
[06:49:54] Found samclip - /usr/local/bin/samclip
[06:49:54] Found seqtk - /usr/local/bin/seqtk
[06:49:54] Found parallel - /usr/local/bin/parallel
[06:49:54] Found freebayes - /usr/local/bin/freebayes
[06:49:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:49:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:49:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:49:54] Found vcfuniq - /usr/local/bin/vcfuniq
[06:49:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:49:54] Found gzip - /bin/gzip
[06:49:54] Found vt - /usr/local/bin/vt
[06:49:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:49:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:49:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:49:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:49:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:49:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:49:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:49:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:50:07] This is snippy 4.6.0Show full stderr[06:50:07] This is snippy 4.6.0
[06:50:07] Written by Torsten Seemann
[06:50:07] Obtained from https://github.com/tseemann/snippy
[06:50:07] Detected operating system: linux
[06:50:07] Enabling bundled linux tools.
[06:50:07] Found bwa - /usr/local/bin/bwa
[06:50:07] Found bcftools - /usr/local/bin/bcftools
[06:50:07] Found samtools - /usr/local/bin/samtools
[06:50:07] Found java - /usr/local/bin/java
[06:50:07] Found snpEff - /usr/local/bin/snpEff
[06:50:07] Found samclip - /usr/local/bin/samclip
[06:50:07] Found seqtk - /usr/local/bin/seqtk
[06:50:07] Found parallel - /usr/local/bin/parallel
[06:50:07] Found freebayes - /usr/local/bin/freebayes
[06:50:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:50:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:50:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:50:07] Found vcfuniq - /usr/local/bin/vcfuniq
[06:50:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:50:07] Found gzip - /bin/gzip
[06:50:07] Found vt - /usr/local/bin/vt
[06:50:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:50:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:50:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:50:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:50:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:50:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:50:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:50:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:12:59] This is snippy 4.6.0Show full stderr[07:12:59] This is snippy 4.6.0
[07:12:59] Written by Torsten Seemann
[07:12:59] Obtained from https://github.com/tseemann/snippy
[07:12:59] Detected operating system: linux
[07:12:59] Enabling bundled linux tools.
[07:12:59] Found bwa - /usr/local/bin/bwa
[07:12:59] Found bcftools - /usr/local/bin/bcftools
[07:12:59] Found samtools - /usr/local/bin/samtools
[07:12:59] Found java - /usr/local/bin/java
[07:12:59] Found snpEff - /usr/local/bin/snpEff
[07:12:59] Found samclip - /usr/local/bin/samclip
[07:12:59] Found seqtk - /usr/local/bin/seqtk
[07:12:59] Found parallel - /usr/local/bin/parallel
[07:12:59] Found freebayes - /usr/local/bin/freebayes
[07:12:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:12:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:12:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:12:59] Found vcfuniq - /usr/local/bin/vcfuniq
[07:12:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:12:59] Found gzip - /bin/gzip
[07:12:59] Found vt - /usr/local/bin/vt
[07:12:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:12:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:13:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:13:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:13:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:13:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:13:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:13:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:25:47] This is snippy 4.6.0Show full stderr[07:25:47] This is snippy 4.6.0
[07:25:47] Written by Torsten Seemann
[07:25:47] Obtained from https://github.com/tseemann/snippy
[07:25:47] Detected operating system: linux
[07:25:47] Enabling bundled linux tools.
[07:25:47] Found bwa - /usr/local/bin/bwa
[07:25:47] Found bcftools - /usr/local/bin/bcftools
[07:25:47] Found samtools - /usr/local/bin/samtools
[07:25:47] Found java - /usr/local/bin/java
[07:25:47] Found snpEff - /usr/local/bin/snpEff
[07:25:47] Found samclip - /usr/local/bin/samclip
[07:25:47] Found seqtk - /usr/local/bin/seqtk
[07:25:47] Found parallel - /usr/local/bin/parallel
[07:25:47] Found freebayes - /usr/local/bin/freebayes
[07:25:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:25:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:25:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:25:47] Found vcfuniq - /usr/local/bin/vcfuniq
[07:25:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:25:47] Found gzip - /bin/gzip
[07:25:47] Found vt - /usr/local/bin/vt
[07:25:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:25:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:25:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:25:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:25:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:25:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:25:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:25:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:26:02] This is snippy 4.6.0Show full stderr[07:26:02] This is snippy 4.6.0
[07:26:02] Written by Torsten Seemann
[07:26:02] Obtained from https://github.com/tseemann/snippy
[07:26:02] Detected operating system: linux
[07:26:02] Enabling bundled linux tools.
[07:26:03] Found bwa - /usr/local/bin/bwa
[07:26:03] Found bcftools - /usr/local/bin/bcftools
[07:26:03] Found samtools - /usr/local/bin/samtools
[07:26:03] Found java - /usr/local/bin/java
[07:26:03] Found snpEff - /usr/local/bin/snpEff
[07:26:03] Found samclip - /usr/local/bin/samclip
[07:26:03] Found seqtk - /usr/local/bin/seqtk
[07:26:03] Found parallel - /usr/local/bin/parallel
[07:26:03] Found freebayes - /usr/local/bin/freebayes
[07:26:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:26:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:26:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:26:03] Found vcfuniq - /usr/local/bin/vcfuniq
[07:26:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:26:03] Found gzip - /bin/gzip
[07:26:03] Found vt - /usr/local/bin/vt
[07:26:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:26:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:26:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:26:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:26:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:26:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:26:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:26:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:26:44] This is snippy 4.6.0Show full stderr[07:26:44] This is snippy 4.6.0
[07:26:44] Written by Torsten Seemann
[07:26:44] Obtained from https://github.com/tseemann/snippy
[07:26:44] Detected operating system: linux
[07:26:44] Enabling bundled linux tools.
[07:26:44] Found bwa - /usr/local/bin/bwa
[07:26:44] Found bcftools - /usr/local/bin/bcftools
[07:26:44] Found samtools - /usr/local/bin/samtools
[07:26:44] Found java - /usr/local/bin/java
[07:26:44] Found snpEff - /usr/local/bin/snpEff
[07:26:44] Found samclip - /usr/local/bin/samclip
[07:26:44] Found seqtk - /usr/local/bin/seqtk
[07:26:44] Found parallel - /usr/local/bin/parallel
[07:26:44] Found freebayes - /usr/local/bin/freebayes
[07:26:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:26:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:26:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:26:45] Found vcfuniq - /usr/local/bin/vcfuniq
[07:26:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:26:45] Found gzip - /bin/gzip
[07:26:45] Found vt - /usr/local/bin/vt
[07:26:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:26:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:26:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:26:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:26:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:26:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:26:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:26:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:51:01] This is snippy 4.6.0Show full stderr[06:51:01] This is snippy 4.6.0
[06:51:01] Written by Torsten Seemann
[06:51:01] Obtained from https://github.com/tseemann/snippy
[06:51:01] Detected operating system: linux
[06:51:01] Enabling bundled linux tools.
[06:51:01] Found bwa - /usr/local/bin/bwa
[06:51:01] Found bcftools - /usr/local/bin/bcftools
[06:51:01] Found samtools - /usr/local/bin/samtools
[06:51:01] Found java - /usr/local/bin/java
[06:51:01] Found snpEff - /usr/local/bin/snpEff
[06:51:01] Found samclip - /usr/local/bin/samclip
[06:51:01] Found seqtk - /usr/local/bin/seqtk
[06:51:01] Found parallel - /usr/local/bin/parallel
[06:51:01] Found freebayes - /usr/local/bin/freebayes
[06:51:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:51:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:51:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:51:01] Found vcfuniq - /usr/local/bin/vcfuniq
[06:51:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:51:01] Found gzip - /bin/gzip
[06:51:01] Found vt - /usr/local/bin/vt
[06:51:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:51:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:51:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:51:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:51:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:51:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:51:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:51:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:51:07] This is snippy 4.6.0Show full stderr[06:51:07] This is snippy 4.6.0
[06:51:07] Written by Torsten Seemann
[06:51:07] Obtained from https://github.com/tseemann/snippy
[06:51:07] Detected operating system: linux
[06:51:07] Enabling bundled linux tools.
[06:51:07] Found bwa - /usr/local/bin/bwa
[06:51:07] Found bcftools - /usr/local/bin/bcftools
[06:51:07] Found samtools - /usr/local/bin/samtools
[06:51:07] Found java - /usr/local/bin/java
[06:51:07] Found snpEff - /usr/local/bin/snpEff
[06:51:07] Found samclip - /usr/local/bin/samclip
[06:51:07] Found seqtk - /usr/local/bin/seqtk
[06:51:07] Found parallel - /usr/local/bin/parallel
[06:51:07] Found freebayes - /usr/local/bin/freebayes
[06:51:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:51:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:51:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:51:07] Found vcfuniq - /usr/local/bin/vcfuniq
[06:51:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:51:07] Found gzip - /bin/gzip
[06:51:07] Found vt - /usr/local/bin/vt
[06:51:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:51:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:51:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:51:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:51:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:51:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:51:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:51:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:51:16] This is snippy 4.6.0Show full stderr[06:51:16] This is snippy 4.6.0
[06:51:16] Written by Torsten Seemann
[06:51:16] Obtained from https://github.com/tseemann/snippy
[06:51:16] Detected operating system: linux
[06:51:16] Enabling bundled linux tools.
[06:51:16] Found bwa - /usr/local/bin/bwa
[06:51:16] Found bcftools - /usr/local/bin/bcftools
[06:51:16] Found samtools - /usr/local/bin/samtools
[06:51:16] Found java - /usr/local/bin/java
[06:51:16] Found snpEff - /usr/local/bin/snpEff
[06:51:16] Found samclip - /usr/local/bin/samclip
[06:51:16] Found seqtk - /usr/local/bin/seqtk
[06:51:16] Found parallel - /usr/local/bin/parallel
[06:51:16] Found freebayes - /usr/local/bin/freebayes
[06:51:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:51:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:51:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:51:16] Found vcfuniq - /usr/local/bin/vcfuniq
[06:51:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:51:16] Found gzip - /bin/gzip
[06:51:16] Found vt - /usr/local/bin/vt
[06:51:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:51:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:51:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:51:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:51:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:51:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:51:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:51:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:52:42] This is snippy 4.6.0Show full stderr[06:52:42] This is snippy 4.6.0
[06:52:42] Written by Torsten Seemann
[06:52:42] Obtained from https://github.com/tseemann/snippy
[06:52:42] Detected operating system: linux
[06:52:42] Enabling bundled linux tools.
[06:52:42] Found bwa - /usr/local/bin/bwa
[06:52:42] Found bcftools - /usr/local/bin/bcftools
[06:52:42] Found samtools - /usr/local/bin/samtools
[06:52:42] Found java - /usr/local/bin/java
[06:52:42] Found snpEff - /usr/local/bin/snpEff
[06:52:42] Found samclip - /usr/local/bin/samclip
[06:52:42] Found seqtk - /usr/local/bin/seqtk
[06:52:42] Found parallel - /usr/local/bin/parallel
[06:52:42] Found freebayes - /usr/local/bin/freebayes
[06:52:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:42] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:42] Found gzip - /bin/gzip
[06:52:42] Found vt - /usr/local/bin/vt
[06:52:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:15:36] This is snippy 4.6.0Show full stderr[08:15:36] This is snippy 4.6.0
[08:15:36] Written by Torsten Seemann
[08:15:36] Obtained from https://github.com/tseemann/snippy
[08:15:36] Detected operating system: linux
[08:15:36] Enabling bundled linux tools.
[08:15:36] Found bwa - /usr/local/bin/bwa
[08:15:36] Found bcftools - /usr/local/bin/bcftools
[08:15:36] Found samtools - /usr/local/bin/samtools
[08:15:36] Found java - /usr/local/bin/java
[08:15:36] Found snpEff - /usr/local/bin/snpEff
[08:15:36] Found samclip - /usr/local/bin/samclip
[08:15:36] Found seqtk - /usr/local/bin/seqtk
[08:15:37] Found parallel - /usr/local/bin/parallel
[08:15:37] Found freebayes - /usr/local/bin/freebayes
[08:15:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:15:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:15:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:15:37] Found vcfuniq - /usr/local/bin/vcfuniq
[08:15:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:15:37] Found gzip - /bin/gzip
[08:15:37] Found vt - /usr/local/bin/vt
[08:15:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:15:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:15:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:15:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:15:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:15:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:15:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:15:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:53:21] This is snippy 4.6.0Show full stderr[06:53:21] This is snippy 4.6.0
[06:53:21] Written by Torsten Seemann
[06:53:21] Obtained from https://github.com/tseemann/snippy
[06:53:21] Detected operating system: linux
[06:53:21] Enabling bundled linux tools.
[06:53:21] Found bwa - /usr/local/bin/bwa
[06:53:21] Found bcftools - /usr/local/bin/bcftools
[06:53:21] Found samtools - /usr/local/bin/samtools
[06:53:21] Found java - /usr/local/bin/java
[06:53:21] Found snpEff - /usr/local/bin/snpEff
[06:53:21] Found samclip - /usr/local/bin/samclip
[06:53:21] Found seqtk - /usr/local/bin/seqtk
[06:53:21] Found parallel - /usr/local/bin/parallel
[06:53:21] Found freebayes - /usr/local/bin/freebayes
[06:53:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:21] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:21] Found gzip - /bin/gzip
[06:53:21] Found vt - /usr/local/bin/vt
[06:53:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:16:29] This is snippy 4.6.0Show full stderr[08:16:29] This is snippy 4.6.0
[08:16:29] Written by Torsten Seemann
[08:16:29] Obtained from https://github.com/tseemann/snippy
[08:16:29] Detected operating system: linux
[08:16:29] Enabling bundled linux tools.
[08:16:29] Found bwa - /usr/local/bin/bwa
[08:16:29] Found bcftools - /usr/local/bin/bcftools
[08:16:29] Found samtools - /usr/local/bin/samtools
[08:16:29] Found java - /usr/local/bin/java
[08:16:29] Found snpEff - /usr/local/bin/snpEff
[08:16:29] Found samclip - /usr/local/bin/samclip
[08:16:29] Found seqtk - /usr/local/bin/seqtk
[08:16:29] Found parallel - /usr/local/bin/parallel
[08:16:29] Found freebayes - /usr/local/bin/freebayes
[08:16:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:16:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:16:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:16:29] Found vcfuniq - /usr/local/bin/vcfuniq
[08:16:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:16:29] Found gzip - /bin/gzip
[08:16:29] Found vt - /usr/local/bin/vt
[08:16:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:16:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:16:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:16:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:16:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:16:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:16:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:16:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:54:40] This is snippy 4.6.0Show full stderr[06:54:40] This is snippy 4.6.0
[06:54:40] Written by Torsten Seemann
[06:54:40] Obtained from https://github.com/tseemann/snippy
[06:54:40] Detected operating system: linux
[06:54:40] Enabling bundled linux tools.
[06:54:40] Found bwa - /usr/local/bin/bwa
[06:54:40] Found bcftools - /usr/local/bin/bcftools
[06:54:40] Found samtools - /usr/local/bin/samtools
[06:54:40] Found java - /usr/local/bin/java
[06:54:40] Found snpEff - /usr/local/bin/snpEff
[06:54:40] Found samclip - /usr/local/bin/samclip
[06:54:40] Found seqtk - /usr/local/bin/seqtk
[06:54:40] Found parallel - /usr/local/bin/parallel
[06:54:40] Found freebayes - /usr/local/bin/freebayes
[06:54:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:40] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:40] Found gzip - /bin/gzip
[06:54:40] Found vt - /usr/local/bin/vt
[06:54:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:50:22] This is snippy 4.6.0Show full stderr[06:50:22] This is snippy 4.6.0
[06:50:22] Written by Torsten Seemann
[06:50:22] Obtained from https://github.com/tseemann/snippy
[06:50:22] Detected operating system: linux
[06:50:22] Enabling bundled linux tools.
[06:50:22] Found bwa - /usr/local/bin/bwa
[06:50:22] Found bcftools - /usr/local/bin/bcftools
[06:50:22] Found samtools - /usr/local/bin/samtools
[06:50:22] Found java - /usr/local/bin/java
[06:50:22] Found snpEff - /usr/local/bin/snpEff
[06:50:22] Found samclip - /usr/local/bin/samclip
[06:50:22] Found seqtk - /usr/local/bin/seqtk
[06:50:22] Found parallel - /usr/local/bin/parallel
[06:50:22] Found freebayes - /usr/local/bin/freebayes
[06:50:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:50:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:50:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:50:22] Found vcfuniq - /usr/local/bin/vcfuniq
[06:50:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:50:22] Found gzip - /bin/gzip
[06:50:22] Found vt - /usr/local/bin/vt
[06:50:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:50:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:50:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:50:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:50:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:50:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:50:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:50:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:51:46] This is snippy 4.6.0Show full stderr[06:51:46] This is snippy 4.6.0
[06:51:46] Written by Torsten Seemann
[06:51:46] Obtained from https://github.com/tseemann/snippy
[06:51:46] Detected operating system: linux
[06:51:46] Enabling bundled linux tools.
[06:51:46] Found bwa - /usr/local/bin/bwa
[06:51:46] Found bcftools - /usr/local/bin/bcftools
[06:51:46] Found samtools - /usr/local/bin/samtools
[06:51:46] Found java - /usr/local/bin/java
[06:51:46] Found snpEff - /usr/local/bin/snpEff
[06:51:46] Found samclip - /usr/local/bin/samclip
[06:51:46] Found seqtk - /usr/local/bin/seqtk
[06:51:46] Found parallel - /usr/local/bin/parallel
[06:51:46] Found freebayes - /usr/local/bin/freebayes
[06:51:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:51:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:51:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:51:46] Found vcfuniq - /usr/local/bin/vcfuniq
[06:51:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:51:46] Found gzip - /bin/gzip
[06:51:46] Found vt - /usr/local/bin/vt
[06:51:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:51:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:51:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:51:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:51:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:51:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:51:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:51:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:52:28] This is snippy 4.6.0Show full stderr[06:52:28] This is snippy 4.6.0
[06:52:28] Written by Torsten Seemann
[06:52:28] Obtained from https://github.com/tseemann/snippy
[06:52:28] Detected operating system: linux
[06:52:28] Enabling bundled linux tools.
[06:52:28] Found bwa - /usr/local/bin/bwa
[06:52:28] Found bcftools - /usr/local/bin/bcftools
[06:52:28] Found samtools - /usr/local/bin/samtools
[06:52:28] Found java - /usr/local/bin/java
[06:52:28] Found snpEff - /usr/local/bin/snpEff
[06:52:28] Found samclip - /usr/local/bin/samclip
[06:52:28] Found seqtk - /usr/local/bin/seqtk
[06:52:28] Found parallel - /usr/local/bin/parallel
[06:52:28] Found freebayes - /usr/local/bin/freebayes
[06:52:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:28] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:28] Found gzip - /bin/gzip
[06:52:28] Found vt - /usr/local/bin/vt
[06:52:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:53:03] This is snippy 4.6.0Show full stderr[06:53:03] This is snippy 4.6.0
[06:53:03] Written by Torsten Seemann
[06:53:03] Obtained from https://github.com/tseemann/snippy
[06:53:03] Detected operating system: linux
[06:53:03] Enabling bundled linux tools.
[06:53:03] Found bwa - /usr/local/bin/bwa
[06:53:03] Found bcftools - /usr/local/bin/bcftools
[06:53:03] Found samtools - /usr/local/bin/samtools
[06:53:03] Found java - /usr/local/bin/java
[06:53:03] Found snpEff - /usr/local/bin/snpEff
[06:53:03] Found samclip - /usr/local/bin/samclip
[06:53:03] Found seqtk - /usr/local/bin/seqtk
[06:53:03] Found parallel - /usr/local/bin/parallel
[06:53:03] Found freebayes - /usr/local/bin/freebayes
[06:53:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:03] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:03] Found gzip - /bin/gzip
[06:53:03] Found vt - /usr/local/bin/vt
[06:53:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:53:24] This is snippy 4.6.0Show full stderr[06:53:24] This is snippy 4.6.0
[06:53:24] Written by Torsten Seemann
[06:53:24] Obtained from https://github.com/tseemann/snippy
[06:53:24] Detected operating system: linux
[06:53:24] Enabling bundled linux tools.
[06:53:24] Found bwa - /usr/local/bin/bwa
[06:53:24] Found bcftools - /usr/local/bin/bcftools
[06:53:24] Found samtools - /usr/local/bin/samtools
[06:53:24] Found java - /usr/local/bin/java
[06:53:24] Found snpEff - /usr/local/bin/snpEff
[06:53:24] Found samclip - /usr/local/bin/samclip
[06:53:24] Found seqtk - /usr/local/bin/seqtk
[06:53:24] Found parallel - /usr/local/bin/parallel
[06:53:24] Found freebayes - /usr/local/bin/freebayes
[06:53:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:24] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:24] Found gzip - /bin/gzip
[06:53:24] Found vt - /usr/local/bin/vt
[06:53:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:51:19] This is snippy 4.6.0Show full stderr[06:51:19] This is snippy 4.6.0
[06:51:19] Written by Torsten Seemann
[06:51:19] Obtained from https://github.com/tseemann/snippy
[06:51:19] Detected operating system: linux
[06:51:19] Enabling bundled linux tools.
[06:51:19] Found bwa - /usr/local/bin/bwa
[06:51:19] Found bcftools - /usr/local/bin/bcftools
[06:51:19] Found samtools - /usr/local/bin/samtools
[06:51:19] Found java - /usr/local/bin/java
[06:51:19] Found snpEff - /usr/local/bin/snpEff
[06:51:19] Found samclip - /usr/local/bin/samclip
[06:51:19] Found seqtk - /usr/local/bin/seqtk
[06:51:19] Found parallel - /usr/local/bin/parallel
[06:51:19] Found freebayes - /usr/local/bin/freebayes
[06:51:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:51:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:51:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:51:19] Found vcfuniq - /usr/local/bin/vcfuniq
[06:51:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:51:19] Found gzip - /bin/gzip
[06:51:19] Found vt - /usr/local/bin/vt
[06:51:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:51:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:51:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:51:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:51:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:51:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:51:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:51:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:51:34] This is snippy 4.6.0Show full stderr[06:51:34] This is snippy 4.6.0
[06:51:34] Written by Torsten Seemann
[06:51:34] Obtained from https://github.com/tseemann/snippy
[06:51:34] Detected operating system: linux
[06:51:34] Enabling bundled linux tools.
[06:51:34] Found bwa - /usr/local/bin/bwa
[06:51:34] Found bcftools - /usr/local/bin/bcftools
[06:51:34] Found samtools - /usr/local/bin/samtools
[06:51:34] Found java - /usr/local/bin/java
[06:51:34] Found snpEff - /usr/local/bin/snpEff
[06:51:34] Found samclip - /usr/local/bin/samclip
[06:51:34] Found seqtk - /usr/local/bin/seqtk
[06:51:34] Found parallel - /usr/local/bin/parallel
[06:51:34] Found freebayes - /usr/local/bin/freebayes
[06:51:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:51:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:51:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:51:34] Found vcfuniq - /usr/local/bin/vcfuniq
[06:51:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:51:34] Found gzip - /bin/gzip
[06:51:34] Found vt - /usr/local/bin/vt
[06:51:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:51:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:51:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:51:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:51:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:51:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:51:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:51:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:52:01] This is snippy 4.6.0Show full stderr[06:52:01] This is snippy 4.6.0
[06:52:01] Written by Torsten Seemann
[06:52:01] Obtained from https://github.com/tseemann/snippy
[06:52:01] Detected operating system: linux
[06:52:01] Enabling bundled linux tools.
[06:52:01] Found bwa - /usr/local/bin/bwa
[06:52:01] Found bcftools - /usr/local/bin/bcftools
[06:52:01] Found samtools - /usr/local/bin/samtools
[06:52:01] Found java - /usr/local/bin/java
[06:52:01] Found snpEff - /usr/local/bin/snpEff
[06:52:01] Found samclip - /usr/local/bin/samclip
[06:52:01] Found seqtk - /usr/local/bin/seqtk
[06:52:01] Found parallel - /usr/local/bin/parallel
[06:52:01] Found freebayes - /usr/local/bin/freebayes
[06:52:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:01] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:01] Found gzip - /bin/gzip
[06:52:01] Found vt - /usr/local/bin/vt
[06:52:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:52:25] This is snippy 4.6.0Show full stderr[06:52:25] This is snippy 4.6.0
[06:52:25] Written by Torsten Seemann
[06:52:25] Obtained from https://github.com/tseemann/snippy
[06:52:25] Detected operating system: linux
[06:52:25] Enabling bundled linux tools.
[06:52:25] Found bwa - /usr/local/bin/bwa
[06:52:25] Found bcftools - /usr/local/bin/bcftools
[06:52:25] Found samtools - /usr/local/bin/samtools
[06:52:25] Found java - /usr/local/bin/java
[06:52:25] Found snpEff - /usr/local/bin/snpEff
[06:52:25] Found samclip - /usr/local/bin/samclip
[06:52:25] Found seqtk - /usr/local/bin/seqtk
[06:52:25] Found parallel - /usr/local/bin/parallel
[06:52:25] Found freebayes - /usr/local/bin/freebayes
[06:52:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:25] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:25] Found gzip - /bin/gzip
[06:52:25] Found vt - /usr/local/bin/vt
[06:52:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:52:39] This is snippy 4.6.0Show full stderr[06:52:39] This is snippy 4.6.0
[06:52:39] Written by Torsten Seemann
[06:52:39] Obtained from https://github.com/tseemann/snippy
[06:52:39] Detected operating system: linux
[06:52:39] Enabling bundled linux tools.
[06:52:39] Found bwa - /usr/local/bin/bwa
[06:52:39] Found bcftools - /usr/local/bin/bcftools
[06:52:39] Found samtools - /usr/local/bin/samtools
[06:52:39] Found java - /usr/local/bin/java
[06:52:39] Found snpEff - /usr/local/bin/snpEff
[06:52:39] Found samclip - /usr/local/bin/samclip
[06:52:39] Found seqtk - /usr/local/bin/seqtk
[06:52:39] Found parallel - /usr/local/bin/parallel
[06:52:39] Found freebayes - /usr/local/bin/freebayes
[06:52:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:39] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:39] Found gzip - /bin/gzip
[06:52:39] Found vt - /usr/local/bin/vt
[06:52:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:52:54] This is snippy 4.6.0Show full stderr[06:52:54] This is snippy 4.6.0
[06:52:54] Written by Torsten Seemann
[06:52:54] Obtained from https://github.com/tseemann/snippy
[06:52:54] Detected operating system: linux
[06:52:54] Enabling bundled linux tools.
[06:52:54] Found bwa - /usr/local/bin/bwa
[06:52:54] Found bcftools - /usr/local/bin/bcftools
[06:52:54] Found samtools - /usr/local/bin/samtools
[06:52:54] Found java - /usr/local/bin/java
[06:52:54] Found snpEff - /usr/local/bin/snpEff
[06:52:54] Found samclip - /usr/local/bin/samclip
[06:52:54] Found seqtk - /usr/local/bin/seqtk
[06:52:54] Found parallel - /usr/local/bin/parallel
[06:52:54] Found freebayes - /usr/local/bin/freebayes
[06:52:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:54] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:54] Found gzip - /bin/gzip
[06:52:54] Found vt - /usr/local/bin/vt
[06:52:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:52:57] This is snippy 4.6.0Show full stderr[06:52:57] This is snippy 4.6.0
[06:52:57] Written by Torsten Seemann
[06:52:57] Obtained from https://github.com/tseemann/snippy
[06:52:57] Detected operating system: linux
[06:52:57] Enabling bundled linux tools.
[06:52:57] Found bwa - /usr/local/bin/bwa
[06:52:57] Found bcftools - /usr/local/bin/bcftools
[06:52:57] Found samtools - /usr/local/bin/samtools
[06:52:57] Found java - /usr/local/bin/java
[06:52:57] Found snpEff - /usr/local/bin/snpEff
[06:52:57] Found samclip - /usr/local/bin/samclip
[06:52:57] Found seqtk - /usr/local/bin/seqtk
[06:52:57] Found parallel - /usr/local/bin/parallel
[06:52:57] Found freebayes - /usr/local/bin/freebayes
[06:52:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:52:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:52:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:52:57] Found vcfuniq - /usr/local/bin/vcfuniq
[06:52:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:52:57] Found gzip - /bin/gzip
[06:52:57] Found vt - /usr/local/bin/vt
[06:52:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:52:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:52:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:52:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:52:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:52:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:52:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:52:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:53:04] This is snippy 4.6.0Show full stderr[06:53:04] This is snippy 4.6.0
[06:53:04] Written by Torsten Seemann
[06:53:04] Obtained from https://github.com/tseemann/snippy
[06:53:04] Detected operating system: linux
[06:53:04] Enabling bundled linux tools.
[06:53:04] Found bwa - /usr/local/bin/bwa
[06:53:04] Found bcftools - /usr/local/bin/bcftools
[06:53:04] Found samtools - /usr/local/bin/samtools
[06:53:04] Found java - /usr/local/bin/java
[06:53:04] Found snpEff - /usr/local/bin/snpEff
[06:53:04] Found samclip - /usr/local/bin/samclip
[06:53:04] Found seqtk - /usr/local/bin/seqtk
[06:53:04] Found parallel - /usr/local/bin/parallel
[06:53:04] Found freebayes - /usr/local/bin/freebayes
[06:53:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:04] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:04] Found gzip - /bin/gzip
[06:53:04] Found vt - /usr/local/bin/vt
[06:53:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:53:07] This is snippy 4.6.0Show full stderr[06:53:07] This is snippy 4.6.0
[06:53:07] Written by Torsten Seemann
[06:53:07] Obtained from https://github.com/tseemann/snippy
[06:53:07] Detected operating system: linux
[06:53:07] Enabling bundled linux tools.
[06:53:07] Found bwa - /usr/local/bin/bwa
[06:53:07] Found bcftools - /usr/local/bin/bcftools
[06:53:07] Found samtools - /usr/local/bin/samtools
[06:53:07] Found java - /usr/local/bin/java
[06:53:07] Found snpEff - /usr/local/bin/snpEff
[06:53:07] Found samclip - /usr/local/bin/samclip
[06:53:07] Found seqtk - /usr/local/bin/seqtk
[06:53:07] Found parallel - /usr/local/bin/parallel
[06:53:07] Found freebayes - /usr/local/bin/freebayes
[06:53:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:07] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:07] Found gzip - /bin/gzip
[06:53:07] Found vt - /usr/local/bin/vt
[06:53:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:53:10] This is snippy 4.6.0Show full stderr[06:53:10] This is snippy 4.6.0
[06:53:10] Written by Torsten Seemann
[06:53:10] Obtained from https://github.com/tseemann/snippy
[06:53:10] Detected operating system: linux
[06:53:10] Enabling bundled linux tools.
[06:53:10] Found bwa - /usr/local/bin/bwa
[06:53:10] Found bcftools - /usr/local/bin/bcftools
[06:53:10] Found samtools - /usr/local/bin/samtools
[06:53:10] Found java - /usr/local/bin/java
[06:53:10] Found snpEff - /usr/local/bin/snpEff
[06:53:10] Found samclip - /usr/local/bin/samclip
[06:53:10] Found seqtk - /usr/local/bin/seqtk
[06:53:10] Found parallel - /usr/local/bin/parallel
[06:53:10] Found freebayes - /usr/local/bin/freebayes
[06:53:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:53:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:53:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:53:10] Found vcfuniq - /usr/local/bin/vcfuniq
[06:53:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:53:10] Found gzip - /bin/gzip
[06:53:10] Found vt - /usr/local/bin/vt
[06:53:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:53:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:53:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:53:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:53:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:53:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:53:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:53:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:54:13] This is snippy 4.6.0Show full stderr[06:54:13] This is snippy 4.6.0
[06:54:13] Written by Torsten Seemann
[06:54:13] Obtained from https://github.com/tseemann/snippy
[06:54:13] Detected operating system: linux
[06:54:13] Enabling bundled linux tools.
[06:54:13] Found bwa - /usr/local/bin/bwa
[06:54:13] Found bcftools - /usr/local/bin/bcftools
[06:54:13] Found samtools - /usr/local/bin/samtools
[06:54:13] Found java - /usr/local/bin/java
[06:54:13] Found snpEff - /usr/local/bin/snpEff
[06:54:13] Found samclip - /usr/local/bin/samclip
[06:54:13] Found seqtk - /usr/local/bin/seqtk
[06:54:13] Found parallel - /usr/local/bin/parallel
[06:54:13] Found freebayes - /usr/local/bin/freebayes
[06:54:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:13] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:13] Found gzip - /bin/gzip
[06:54:13] Found vt - /usr/local/bin/vt
[06:54:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:50:49] This is snippy 4.6.0Show full stderr[07:50:49] This is snippy 4.6.0
[07:50:49] Written by Torsten Seemann
[07:50:49] Obtained from https://github.com/tseemann/snippy
[07:50:49] Detected operating system: linux
[07:50:49] Enabling bundled linux tools.
[07:50:49] Found bwa - /usr/local/bin/bwa
[07:50:49] Found bcftools - /usr/local/bin/bcftools
[07:50:49] Found samtools - /usr/local/bin/samtools
[07:50:49] Found java - /usr/local/bin/java
[07:50:49] Found snpEff - /usr/local/bin/snpEff
[07:50:49] Found samclip - /usr/local/bin/samclip
[07:50:49] Found seqtk - /usr/local/bin/seqtk
[07:50:49] Found parallel - /usr/local/bin/parallel
[07:50:49] Found freebayes - /usr/local/bin/freebayes
[07:50:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:50:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:50:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:50:49] Found vcfuniq - /usr/local/bin/vcfuniq
[07:50:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:50:49] Found gzip - /bin/gzip
[07:50:49] Found vt - /usr/local/bin/vt
[07:50:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:50:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:50:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:50:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:50:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:50:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:50:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:50:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:56:01] This is snippy 4.6.0Show full stderr[06:56:01] This is snippy 4.6.0
[06:56:01] Written by Torsten Seemann
[06:56:01] Obtained from https://github.com/tseemann/snippy
[06:56:01] Detected operating system: linux
[06:56:01] Enabling bundled linux tools.
[06:56:01] Found bwa - /usr/local/bin/bwa
[06:56:01] Found bcftools - /usr/local/bin/bcftools
[06:56:01] Found samtools - /usr/local/bin/samtools
[06:56:01] Found java - /usr/local/bin/java
[06:56:01] Found snpEff - /usr/local/bin/snpEff
[06:56:01] Found samclip - /usr/local/bin/samclip
[06:56:01] Found seqtk - /usr/local/bin/seqtk
[06:56:01] Found parallel - /usr/local/bin/parallel
[06:56:01] Found freebayes - /usr/local/bin/freebayes
[06:56:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:56:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:56:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:56:01] Found vcfuniq - /usr/local/bin/vcfuniq
[06:56:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:56:01] Found gzip - /bin/gzip
[06:56:01] Found vt - /usr/local/bin/vt
[06:56:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:56:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:56:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:56:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:56:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:56:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:56:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:56:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:58:00] This is snippy 4.6.0Show full stderr[06:58:00] This is snippy 4.6.0
[06:58:00] Written by Torsten Seemann
[06:58:00] Obtained from https://github.com/tseemann/snippy
[06:58:00] Detected operating system: linux
[06:58:00] Enabling bundled linux tools.
[06:58:00] Found bwa - /usr/local/bin/bwa
[06:58:00] Found bcftools - /usr/local/bin/bcftools
[06:58:00] Found samtools - /usr/local/bin/samtools
[06:58:00] Found java - /usr/local/bin/java
[06:58:00] Found snpEff - /usr/local/bin/snpEff
[06:58:00] Found samclip - /usr/local/bin/samclip
[06:58:00] Found seqtk - /usr/local/bin/seqtk
[06:58:00] Found parallel - /usr/local/bin/parallel
[06:58:00] Found freebayes - /usr/local/bin/freebayes
[06:58:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:00] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:00] Found gzip - /bin/gzip
[06:58:00] Found vt - /usr/local/bin/vt
[06:58:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:58:14] This is snippy 4.6.0Show full stderr[06:58:14] This is snippy 4.6.0
[06:58:14] Written by Torsten Seemann
[06:58:14] Obtained from https://github.com/tseemann/snippy
[06:58:14] Detected operating system: linux
[06:58:14] Enabling bundled linux tools.
[06:58:14] Found bwa - /usr/local/bin/bwa
[06:58:14] Found bcftools - /usr/local/bin/bcftools
[06:58:14] Found samtools - /usr/local/bin/samtools
[06:58:14] Found java - /usr/local/bin/java
[06:58:14] Found snpEff - /usr/local/bin/snpEff
[06:58:14] Found samclip - /usr/local/bin/samclip
[06:58:14] Found seqtk - /usr/local/bin/seqtk
[06:58:14] Found parallel - /usr/local/bin/parallel
[06:58:14] Found freebayes - /usr/local/bin/freebayes
[06:58:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:14] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:14] Found gzip - /bin/gzip
[06:58:14] Found vt - /usr/local/bin/vt
[06:58:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:21:38] This is snippy 4.6.0Show full stderr[08:21:38] This is snippy 4.6.0
[08:21:38] Written by Torsten Seemann
[08:21:38] Obtained from https://github.com/tseemann/snippy
[08:21:38] Detected operating system: linux
[08:21:38] Enabling bundled linux tools.
[08:21:38] Found bwa - /usr/local/bin/bwa
[08:21:38] Found bcftools - /usr/local/bin/bcftools
[08:21:38] Found samtools - /usr/local/bin/samtools
[08:21:38] Found java - /usr/local/bin/java
[08:21:38] Found snpEff - /usr/local/bin/snpEff
[08:21:38] Found samclip - /usr/local/bin/samclip
[08:21:38] Found seqtk - /usr/local/bin/seqtk
[08:21:38] Found parallel - /usr/local/bin/parallel
[08:21:38] Found freebayes - /usr/local/bin/freebayes
[08:21:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:21:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:21:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:21:38] Found vcfuniq - /usr/local/bin/vcfuniq
[08:21:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:21:38] Found gzip - /bin/gzip
[08:21:38] Found vt - /usr/local/bin/vt
[08:21:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:21:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:21:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:21:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:21:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:21:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:21:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:21:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:22:39] This is snippy 4.6.0Show full stderr[08:22:39] This is snippy 4.6.0
[08:22:39] Written by Torsten Seemann
[08:22:39] Obtained from https://github.com/tseemann/snippy
[08:22:39] Detected operating system: linux
[08:22:39] Enabling bundled linux tools.
[08:22:39] Found bwa - /usr/local/bin/bwa
[08:22:39] Found bcftools - /usr/local/bin/bcftools
[08:22:39] Found samtools - /usr/local/bin/samtools
[08:22:39] Found java - /usr/local/bin/java
[08:22:39] Found snpEff - /usr/local/bin/snpEff
[08:22:39] Found samclip - /usr/local/bin/samclip
[08:22:39] Found seqtk - /usr/local/bin/seqtk
[08:22:39] Found parallel - /usr/local/bin/parallel
[08:22:39] Found freebayes - /usr/local/bin/freebayes
[08:22:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:22:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:22:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:22:39] Found vcfuniq - /usr/local/bin/vcfuniq
[08:22:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:22:39] Found gzip - /bin/gzip
[08:22:39] Found vt - /usr/local/bin/vt
[08:22:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:22:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:22:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:22:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:22:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:22:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:22:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:22:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:55:13] This is snippy 4.6.0Show full stderr[06:55:13] This is snippy 4.6.0
[06:55:13] Written by Torsten Seemann
[06:55:13] Obtained from https://github.com/tseemann/snippy
[06:55:13] Detected operating system: linux
[06:55:13] Enabling bundled linux tools.
[06:55:13] Found bwa - /usr/local/bin/bwa
[06:55:13] Found bcftools - /usr/local/bin/bcftools
[06:55:13] Found samtools - /usr/local/bin/samtools
[06:55:13] Found java - /usr/local/bin/java
[06:55:13] Found snpEff - /usr/local/bin/snpEff
[06:55:13] Found samclip - /usr/local/bin/samclip
[06:55:13] Found seqtk - /usr/local/bin/seqtk
[06:55:13] Found parallel - /usr/local/bin/parallel
[06:55:13] Found freebayes - /usr/local/bin/freebayes
[06:55:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:13] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:13] Found gzip - /bin/gzip
[06:55:13] Found vt - /usr/local/bin/vt
[06:55:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:55:43] This is snippy 4.6.0Show full stderr[06:55:43] This is snippy 4.6.0
[06:55:43] Written by Torsten Seemann
[06:55:43] Obtained from https://github.com/tseemann/snippy
[06:55:43] Detected operating system: linux
[06:55:43] Enabling bundled linux tools.
[06:55:43] Found bwa - /usr/local/bin/bwa
[06:55:43] Found bcftools - /usr/local/bin/bcftools
[06:55:43] Found samtools - /usr/local/bin/samtools
[06:55:43] Found java - /usr/local/bin/java
[06:55:43] Found snpEff - /usr/local/bin/snpEff
[06:55:43] Found samclip - /usr/local/bin/samclip
[06:55:43] Found seqtk - /usr/local/bin/seqtk
[06:55:43] Found parallel - /usr/local/bin/parallel
[06:55:43] Found freebayes - /usr/local/bin/freebayes
[06:55:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:43] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:43] Found gzip - /bin/gzip
[06:55:43] Found vt - /usr/local/bin/vt
[06:55:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:56:04] This is snippy 4.6.0Show full stderr[06:56:04] This is snippy 4.6.0
[06:56:04] Written by Torsten Seemann
[06:56:04] Obtained from https://github.com/tseemann/snippy
[06:56:04] Detected operating system: linux
[06:56:04] Enabling bundled linux tools.
[06:56:04] Found bwa - /usr/local/bin/bwa
[06:56:04] Found bcftools - /usr/local/bin/bcftools
[06:56:04] Found samtools - /usr/local/bin/samtools
[06:56:04] Found java - /usr/local/bin/java
[06:56:04] Found snpEff - /usr/local/bin/snpEff
[06:56:04] Found samclip - /usr/local/bin/samclip
[06:56:04] Found seqtk - /usr/local/bin/seqtk
[06:56:04] Found parallel - /usr/local/bin/parallel
[06:56:04] Found freebayes - /usr/local/bin/freebayes
[06:56:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:56:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:56:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:56:04] Found vcfuniq - /usr/local/bin/vcfuniq
[06:56:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:56:04] Found gzip - /bin/gzip
[06:56:04] Found vt - /usr/local/bin/vt
[06:56:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:56:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:56:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:56:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:56:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:56:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:56:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:56:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:56:44] This is snippy 4.6.0Show full stderr[06:56:44] This is snippy 4.6.0
[06:56:44] Written by Torsten Seemann
[06:56:44] Obtained from https://github.com/tseemann/snippy
[06:56:44] Detected operating system: linux
[06:56:44] Enabling bundled linux tools.
[06:56:44] Found bwa - /usr/local/bin/bwa
[06:56:44] Found bcftools - /usr/local/bin/bcftools
[06:56:44] Found samtools - /usr/local/bin/samtools
[06:56:44] Found java - /usr/local/bin/java
[06:56:44] Found snpEff - /usr/local/bin/snpEff
[06:56:44] Found samclip - /usr/local/bin/samclip
[06:56:44] Found seqtk - /usr/local/bin/seqtk
[06:56:44] Found parallel - /usr/local/bin/parallel
[06:56:44] Found freebayes - /usr/local/bin/freebayes
[06:56:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:56:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:56:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:56:44] Found vcfuniq - /usr/local/bin/vcfuniq
[06:56:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:56:44] Found gzip - /bin/gzip
[06:56:44] Found vt - /usr/local/bin/vt
[06:56:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:56:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:56:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:56:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:56:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:56:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:56:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:56:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:54:25] This is snippy 4.6.0Show full stderr[06:54:25] This is snippy 4.6.0
[06:54:25] Written by Torsten Seemann
[06:54:25] Obtained from https://github.com/tseemann/snippy
[06:54:25] Detected operating system: linux
[06:54:25] Enabling bundled linux tools.
[06:54:25] Found bwa - /usr/local/bin/bwa
[06:54:25] Found bcftools - /usr/local/bin/bcftools
[06:54:25] Found samtools - /usr/local/bin/samtools
[06:54:25] Found java - /usr/local/bin/java
[06:54:25] Found snpEff - /usr/local/bin/snpEff
[06:54:25] Found samclip - /usr/local/bin/samclip
[06:54:25] Found seqtk - /usr/local/bin/seqtk
[06:54:25] Found parallel - /usr/local/bin/parallel
[06:54:25] Found freebayes - /usr/local/bin/freebayes
[06:54:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:25] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:25] Found gzip - /bin/gzip
[06:54:25] Found vt - /usr/local/bin/vt
[06:54:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:54:58] This is snippy 4.6.0Show full stderr[06:54:58] This is snippy 4.6.0
[06:54:58] Written by Torsten Seemann
[06:54:58] Obtained from https://github.com/tseemann/snippy
[06:54:58] Detected operating system: linux
[06:54:58] Enabling bundled linux tools.
[06:54:58] Found bwa - /usr/local/bin/bwa
[06:54:58] Found bcftools - /usr/local/bin/bcftools
[06:54:58] Found samtools - /usr/local/bin/samtools
[06:54:58] Found java - /usr/local/bin/java
[06:54:58] Found snpEff - /usr/local/bin/snpEff
[06:54:58] Found samclip - /usr/local/bin/samclip
[06:54:58] Found seqtk - /usr/local/bin/seqtk
[06:54:58] Found parallel - /usr/local/bin/parallel
[06:54:58] Found freebayes - /usr/local/bin/freebayes
[06:54:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:58] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:58] Found gzip - /bin/gzip
[06:54:58] Found vt - /usr/local/bin/vt
[06:54:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:56:18] This is snippy 4.6.0Show full stderr[06:56:18] This is snippy 4.6.0
[06:56:18] Written by Torsten Seemann
[06:56:18] Obtained from https://github.com/tseemann/snippy
[06:56:18] Detected operating system: linux
[06:56:18] Enabling bundled linux tools.
[06:56:18] Found bwa - /usr/local/bin/bwa
[06:56:18] Found bcftools - /usr/local/bin/bcftools
[06:56:18] Found samtools - /usr/local/bin/samtools
[06:56:18] Found java - /usr/local/bin/java
[06:56:18] Found snpEff - /usr/local/bin/snpEff
[06:56:18] Found samclip - /usr/local/bin/samclip
[06:56:18] Found seqtk - /usr/local/bin/seqtk
[06:56:18] Found parallel - /usr/local/bin/parallel
[06:56:18] Found freebayes - /usr/local/bin/freebayes
[06:56:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:56:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:56:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:56:18] Found vcfuniq - /usr/local/bin/vcfuniq
[06:56:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:56:18] Found gzip - /bin/gzip
[06:56:18] Found vt - /usr/local/bin/vt
[06:56:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:56:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:56:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:56:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:56:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:56:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:56:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:56:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:54:10] This is snippy 4.6.0Show full stderr[06:54:10] This is snippy 4.6.0
[06:54:10] Written by Torsten Seemann
[06:54:10] Obtained from https://github.com/tseemann/snippy
[06:54:10] Detected operating system: linux
[06:54:10] Enabling bundled linux tools.
[06:54:10] Found bwa - /usr/local/bin/bwa
[06:54:10] Found bcftools - /usr/local/bin/bcftools
[06:54:10] Found samtools - /usr/local/bin/samtools
[06:54:10] Found java - /usr/local/bin/java
[06:54:10] Found snpEff - /usr/local/bin/snpEff
[06:54:10] Found samclip - /usr/local/bin/samclip
[06:54:10] Found seqtk - /usr/local/bin/seqtk
[06:54:10] Found parallel - /usr/local/bin/parallel
[06:54:10] Found freebayes - /usr/local/bin/freebayes
[06:54:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:54:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:54:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:54:10] Found vcfuniq - /usr/local/bin/vcfuniq
[06:54:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:54:10] Found gzip - /bin/gzip
[06:54:10] Found vt - /usr/local/bin/vt
[06:54:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:54:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:54:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:54:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:54:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:54:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:54:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:54:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:55:25] This is snippy 4.6.0Show full stderr[06:55:25] This is snippy 4.6.0
[06:55:25] Written by Torsten Seemann
[06:55:25] Obtained from https://github.com/tseemann/snippy
[06:55:25] Detected operating system: linux
[06:55:25] Enabling bundled linux tools.
[06:55:25] Found bwa - /usr/local/bin/bwa
[06:55:25] Found bcftools - /usr/local/bin/bcftools
[06:55:25] Found samtools - /usr/local/bin/samtools
[06:55:25] Found java - /usr/local/bin/java
[06:55:25] Found snpEff - /usr/local/bin/snpEff
[06:55:25] Found samclip - /usr/local/bin/samclip
[06:55:25] Found seqtk - /usr/local/bin/seqtk
[06:55:25] Found parallel - /usr/local/bin/parallel
[06:55:25] Found freebayes - /usr/local/bin/freebayes
[06:55:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:25] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:25] Found gzip - /bin/gzip
[06:55:25] Found vt - /usr/local/bin/vt
[06:55:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:55:28] This is snippy 4.6.0Show full stderr[06:55:28] This is snippy 4.6.0
[06:55:28] Written by Torsten Seemann
[06:55:28] Obtained from https://github.com/tseemann/snippy
[06:55:28] Detected operating system: linux
[06:55:28] Enabling bundled linux tools.
[06:55:28] Found bwa - /usr/local/bin/bwa
[06:55:28] Found bcftools - /usr/local/bin/bcftools
[06:55:28] Found samtools - /usr/local/bin/samtools
[06:55:28] Found java - /usr/local/bin/java
[06:55:28] Found snpEff - /usr/local/bin/snpEff
[06:55:28] Found samclip - /usr/local/bin/samclip
[06:55:28] Found seqtk - /usr/local/bin/seqtk
[06:55:28] Found parallel - /usr/local/bin/parallel
[06:55:28] Found freebayes - /usr/local/bin/freebayes
[06:55:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:28] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:28] Found gzip - /bin/gzip
[06:55:28] Found vt - /usr/local/bin/vt
[06:55:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:55:34] This is snippy 4.6.0Show full stderr[06:55:34] This is snippy 4.6.0
[06:55:34] Written by Torsten Seemann
[06:55:34] Obtained from https://github.com/tseemann/snippy
[06:55:34] Detected operating system: linux
[06:55:34] Enabling bundled linux tools.
[06:55:34] Found bwa - /usr/local/bin/bwa
[06:55:34] Found bcftools - /usr/local/bin/bcftools
[06:55:34] Found samtools - /usr/local/bin/samtools
[06:55:34] Found java - /usr/local/bin/java
[06:55:34] Found snpEff - /usr/local/bin/snpEff
[06:55:34] Found samclip - /usr/local/bin/samclip
[06:55:34] Found seqtk - /usr/local/bin/seqtk
[06:55:34] Found parallel - /usr/local/bin/parallel
[06:55:34] Found freebayes - /usr/local/bin/freebayes
[06:55:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:34] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:34] Found gzip - /bin/gzip
[06:55:34] Found vt - /usr/local/bin/vt
[06:55:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:55:46] This is snippy 4.6.0Show full stderr[06:55:46] This is snippy 4.6.0
[06:55:46] Written by Torsten Seemann
[06:55:46] Obtained from https://github.com/tseemann/snippy
[06:55:46] Detected operating system: linux
[06:55:46] Enabling bundled linux tools.
[06:55:46] Found bwa - /usr/local/bin/bwa
[06:55:46] Found bcftools - /usr/local/bin/bcftools
[06:55:46] Found samtools - /usr/local/bin/samtools
[06:55:46] Found java - /usr/local/bin/java
[06:55:46] Found snpEff - /usr/local/bin/snpEff
[06:55:46] Found samclip - /usr/local/bin/samclip
[06:55:46] Found seqtk - /usr/local/bin/seqtk
[06:55:46] Found parallel - /usr/local/bin/parallel
[06:55:46] Found freebayes - /usr/local/bin/freebayes
[06:55:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:46] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:46] Found gzip - /bin/gzip
[06:55:46] Found vt - /usr/local/bin/vt
[06:55:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:56:14] This is snippy 4.6.0Show full stderr[06:56:14] This is snippy 4.6.0
[06:56:14] Written by Torsten Seemann
[06:56:14] Obtained from https://github.com/tseemann/snippy
[06:56:14] Detected operating system: linux
[06:56:14] Enabling bundled linux tools.
[06:56:14] Found bwa - /usr/local/bin/bwa
[06:56:14] Found bcftools - /usr/local/bin/bcftools
[06:56:14] Found samtools - /usr/local/bin/samtools
[06:56:14] Found java - /usr/local/bin/java
[06:56:14] Found snpEff - /usr/local/bin/snpEff
[06:56:14] Found samclip - /usr/local/bin/samclip
[06:56:14] Found seqtk - /usr/local/bin/seqtk
[06:56:14] Found parallel - /usr/local/bin/parallel
[06:56:14] Found freebayes - /usr/local/bin/freebayes
[06:56:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:56:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:56:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:56:14] Found vcfuniq - /usr/local/bin/vcfuniq
[06:56:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:56:14] Found gzip - /bin/gzip
[06:56:14] Found vt - /usr/local/bin/vt
[06:56:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:56:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:56:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:56:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:56:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:56:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:56:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:56:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:32:12] This is snippy 4.6.0Show full stderr[07:32:12] This is snippy 4.6.0
[07:32:12] Written by Torsten Seemann
[07:32:12] Obtained from https://github.com/tseemann/snippy
[07:32:12] Detected operating system: linux
[07:32:12] Enabling bundled linux tools.
[07:32:12] Found bwa - /usr/local/bin/bwa
[07:32:12] Found bcftools - /usr/local/bin/bcftools
[07:32:12] Found samtools - /usr/local/bin/samtools
[07:32:12] Found java - /usr/local/bin/java
[07:32:12] Found snpEff - /usr/local/bin/snpEff
[07:32:12] Found samclip - /usr/local/bin/samclip
[07:32:12] Found seqtk - /usr/local/bin/seqtk
[07:32:12] Found parallel - /usr/local/bin/parallel
[07:32:12] Found freebayes - /usr/local/bin/freebayes
[07:32:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:12] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:12] Found gzip - /bin/gzip
[07:32:12] Found vt - /usr/local/bin/vt
[07:32:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:56:30] This is snippy 4.6.0Show full stderr[06:56:30] This is snippy 4.6.0
[06:56:30] Written by Torsten Seemann
[06:56:30] Obtained from https://github.com/tseemann/snippy
[06:56:30] Detected operating system: linux
[06:56:30] Enabling bundled linux tools.
[06:56:30] Found bwa - /usr/local/bin/bwa
[06:56:30] Found bcftools - /usr/local/bin/bcftools
[06:56:30] Found samtools - /usr/local/bin/samtools
[06:56:30] Found java - /usr/local/bin/java
[06:56:30] Found snpEff - /usr/local/bin/snpEff
[06:56:30] Found samclip - /usr/local/bin/samclip
[06:56:30] Found seqtk - /usr/local/bin/seqtk
[06:56:30] Found parallel - /usr/local/bin/parallel
[06:56:30] Found freebayes - /usr/local/bin/freebayes
[06:56:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:56:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:56:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:56:30] Found vcfuniq - /usr/local/bin/vcfuniq
[06:56:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:56:30] Found gzip - /bin/gzip
[06:56:30] Found vt - /usr/local/bin/vt
[06:56:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:56:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:56:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:56:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:56:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:56:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:56:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:56:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:32:55] This is snippy 4.6.0Show full stderr[07:32:55] This is snippy 4.6.0
[07:32:55] Written by Torsten Seemann
[07:32:55] Obtained from https://github.com/tseemann/snippy
[07:32:55] Detected operating system: linux
[07:32:55] Enabling bundled linux tools.
[07:32:55] Found bwa - /usr/local/bin/bwa
[07:32:55] Found bcftools - /usr/local/bin/bcftools
[07:32:55] Found samtools - /usr/local/bin/samtools
[07:32:55] Found java - /usr/local/bin/java
[07:32:55] Found snpEff - /usr/local/bin/snpEff
[07:32:55] Found samclip - /usr/local/bin/samclip
[07:32:55] Found seqtk - /usr/local/bin/seqtk
[07:32:55] Found parallel - /usr/local/bin/parallel
[07:32:55] Found freebayes - /usr/local/bin/freebayes
[07:32:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:55] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:55] Found gzip - /bin/gzip
[07:32:55] Found vt - /usr/local/bin/vt
[07:32:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:58:35] This is snippy 4.6.0Show full stderr[06:58:35] This is snippy 4.6.0
[06:58:35] Written by Torsten Seemann
[06:58:35] Obtained from https://github.com/tseemann/snippy
[06:58:35] Detected operating system: linux
[06:58:35] Enabling bundled linux tools.
[06:58:35] Found bwa - /usr/local/bin/bwa
[06:58:35] Found bcftools - /usr/local/bin/bcftools
[06:58:35] Found samtools - /usr/local/bin/samtools
[06:58:35] Found java - /usr/local/bin/java
[06:58:35] Found snpEff - /usr/local/bin/snpEff
[06:58:35] Found samclip - /usr/local/bin/samclip
[06:58:35] Found seqtk - /usr/local/bin/seqtk
[06:58:35] Found parallel - /usr/local/bin/parallel
[06:58:35] Found freebayes - /usr/local/bin/freebayes
[06:58:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:35] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:35] Found gzip - /bin/gzip
[06:58:35] Found vt - /usr/local/bin/vt
[06:58:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:58:45] This is snippy 4.6.0Show full stderr[06:58:45] This is snippy 4.6.0
[06:58:45] Written by Torsten Seemann
[06:58:45] Obtained from https://github.com/tseemann/snippy
[06:58:45] Detected operating system: linux
[06:58:45] Enabling bundled linux tools.
[06:58:45] Found bwa - /usr/local/bin/bwa
[06:58:45] Found bcftools - /usr/local/bin/bcftools
[06:58:45] Found samtools - /usr/local/bin/samtools
[06:58:45] Found java - /usr/local/bin/java
[06:58:45] Found snpEff - /usr/local/bin/snpEff
[06:58:46] Found samclip - /usr/local/bin/samclip
[06:58:46] Found seqtk - /usr/local/bin/seqtk
[06:58:46] Found parallel - /usr/local/bin/parallel
[06:58:46] Found freebayes - /usr/local/bin/freebayes
[06:58:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:46] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:46] Found gzip - /bin/gzip
[06:58:46] Found vt - /usr/local/bin/vt
[06:58:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:58:48] This is snippy 4.6.0Show full stderr[06:58:48] This is snippy 4.6.0
[06:58:48] Written by Torsten Seemann
[06:58:48] Obtained from https://github.com/tseemann/snippy
[06:58:48] Detected operating system: linux
[06:58:48] Enabling bundled linux tools.
[06:58:48] Found bwa - /usr/local/bin/bwa
[06:58:48] Found bcftools - /usr/local/bin/bcftools
[06:58:48] Found samtools - /usr/local/bin/samtools
[06:58:48] Found java - /usr/local/bin/java
[06:58:48] Found snpEff - /usr/local/bin/snpEff
[06:58:48] Found samclip - /usr/local/bin/samclip
[06:58:49] Found seqtk - /usr/local/bin/seqtk
[06:58:49] Found parallel - /usr/local/bin/parallel
[06:58:49] Found freebayes - /usr/local/bin/freebayes
[06:58:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:49] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:49] Found gzip - /bin/gzip
[06:58:49] Found vt - /usr/local/bin/vt
[06:58:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:59:04] This is snippy 4.6.0Show full stderr[06:59:04] This is snippy 4.6.0
[06:59:04] Written by Torsten Seemann
[06:59:04] Obtained from https://github.com/tseemann/snippy
[06:59:04] Detected operating system: linux
[06:59:04] Enabling bundled linux tools.
[06:59:04] Found bwa - /usr/local/bin/bwa
[06:59:04] Found bcftools - /usr/local/bin/bcftools
[06:59:04] Found samtools - /usr/local/bin/samtools
[06:59:04] Found java - /usr/local/bin/java
[06:59:04] Found snpEff - /usr/local/bin/snpEff
[06:59:04] Found samclip - /usr/local/bin/samclip
[06:59:04] Found seqtk - /usr/local/bin/seqtk
[06:59:04] Found parallel - /usr/local/bin/parallel
[06:59:04] Found freebayes - /usr/local/bin/freebayes
[06:59:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:04] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:04] Found gzip - /bin/gzip
[06:59:04] Found vt - /usr/local/bin/vt
[06:59:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:59:13] This is snippy 4.6.0Show full stderr[06:59:13] This is snippy 4.6.0
[06:59:13] Written by Torsten Seemann
[06:59:13] Obtained from https://github.com/tseemann/snippy
[06:59:13] Detected operating system: linux
[06:59:13] Enabling bundled linux tools.
[06:59:13] Found bwa - /usr/local/bin/bwa
[06:59:13] Found bcftools - /usr/local/bin/bcftools
[06:59:13] Found samtools - /usr/local/bin/samtools
[06:59:13] Found java - /usr/local/bin/java
[06:59:13] Found snpEff - /usr/local/bin/snpEff
[06:59:13] Found samclip - /usr/local/bin/samclip
[06:59:13] Found seqtk - /usr/local/bin/seqtk
[06:59:13] Found parallel - /usr/local/bin/parallel
[06:59:13] Found freebayes - /usr/local/bin/freebayes
[06:59:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:13] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:13] Found gzip - /bin/gzip
[06:59:13] Found vt - /usr/local/bin/vt
[06:59:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:00:13] This is snippy 4.6.0Show full stderr[07:00:13] This is snippy 4.6.0
[07:00:13] Written by Torsten Seemann
[07:00:13] Obtained from https://github.com/tseemann/snippy
[07:00:13] Detected operating system: linux
[07:00:13] Enabling bundled linux tools.
[07:00:13] Found bwa - /usr/local/bin/bwa
[07:00:13] Found bcftools - /usr/local/bin/bcftools
[07:00:13] Found samtools - /usr/local/bin/samtools
[07:00:13] Found java - /usr/local/bin/java
[07:00:13] Found snpEff - /usr/local/bin/snpEff
[07:00:13] Found samclip - /usr/local/bin/samclip
[07:00:13] Found seqtk - /usr/local/bin/seqtk
[07:00:13] Found parallel - /usr/local/bin/parallel
[07:00:13] Found freebayes - /usr/local/bin/freebayes
[07:00:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:13] Found gzip - /bin/gzip
[07:00:13] Found vt - /usr/local/bin/vt
[07:00:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:51:04] This is snippy 4.6.0Show full stderr[07:51:04] This is snippy 4.6.0
[07:51:04] Written by Torsten Seemann
[07:51:04] Obtained from https://github.com/tseemann/snippy
[07:51:04] Detected operating system: linux
[07:51:04] Enabling bundled linux tools.
[07:51:04] Found bwa - /usr/local/bin/bwa
[07:51:04] Found bcftools - /usr/local/bin/bcftools
[07:51:04] Found samtools - /usr/local/bin/samtools
[07:51:04] Found java - /usr/local/bin/java
[07:51:04] Found snpEff - /usr/local/bin/snpEff
[07:51:04] Found samclip - /usr/local/bin/samclip
[07:51:04] Found seqtk - /usr/local/bin/seqtk
[07:51:04] Found parallel - /usr/local/bin/parallel
[07:51:04] Found freebayes - /usr/local/bin/freebayes
[07:51:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:51:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:51:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:51:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:51:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:51:04] Found gzip - /bin/gzip
[07:51:04] Found vt - /usr/local/bin/vt
[07:51:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:51:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:51:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:51:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:51:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:51:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:51:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:51:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:00:49] This is snippy 4.6.0Show full stderr[07:00:49] This is snippy 4.6.0
[07:00:49] Written by Torsten Seemann
[07:00:49] Obtained from https://github.com/tseemann/snippy
[07:00:49] Detected operating system: linux
[07:00:49] Enabling bundled linux tools.
[07:00:49] Found bwa - /usr/local/bin/bwa
[07:00:49] Found bcftools - /usr/local/bin/bcftools
[07:00:49] Found samtools - /usr/local/bin/samtools
[07:00:49] Found java - /usr/local/bin/java
[07:00:49] Found snpEff - /usr/local/bin/snpEff
[07:00:49] Found samclip - /usr/local/bin/samclip
[07:00:49] Found seqtk - /usr/local/bin/seqtk
[07:00:49] Found parallel - /usr/local/bin/parallel
[07:00:49] Found freebayes - /usr/local/bin/freebayes
[07:00:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:49] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:49] Found gzip - /bin/gzip
[07:00:49] Found vt - /usr/local/bin/vt
[07:00:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:57:22] This is snippy 4.6.0Show full stderr[07:57:22] This is snippy 4.6.0
[07:57:22] Written by Torsten Seemann
[07:57:22] Obtained from https://github.com/tseemann/snippy
[07:57:22] Detected operating system: linux
[07:57:22] Enabling bundled linux tools.
[07:57:22] Found bwa - /usr/local/bin/bwa
[07:57:22] Found bcftools - /usr/local/bin/bcftools
[07:57:22] Found samtools - /usr/local/bin/samtools
[07:57:22] Found java - /usr/local/bin/java
[07:57:22] Found snpEff - /usr/local/bin/snpEff
[07:57:22] Found samclip - /usr/local/bin/samclip
[07:57:22] Found seqtk - /usr/local/bin/seqtk
[07:57:22] Found parallel - /usr/local/bin/parallel
[07:57:22] Found freebayes - /usr/local/bin/freebayes
[07:57:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:57:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:57:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:57:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:57:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:57:22] Found gzip - /bin/gzip
[07:57:22] Found vt - /usr/local/bin/vt
[07:57:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:57:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:57:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:57:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:57:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:57:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:57:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:57:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:57:36] This is snippy 4.6.0Show full stderr[06:57:36] This is snippy 4.6.0
[06:57:36] Written by Torsten Seemann
[06:57:36] Obtained from https://github.com/tseemann/snippy
[06:57:36] Detected operating system: linux
[06:57:36] Enabling bundled linux tools.
[06:57:36] Found bwa - /usr/local/bin/bwa
[06:57:36] Found bcftools - /usr/local/bin/bcftools
[06:57:36] Found samtools - /usr/local/bin/samtools
[06:57:36] Found java - /usr/local/bin/java
[06:57:36] Found snpEff - /usr/local/bin/snpEff
[06:57:36] Found samclip - /usr/local/bin/samclip
[06:57:36] Found seqtk - /usr/local/bin/seqtk
[06:57:36] Found parallel - /usr/local/bin/parallel
[06:57:36] Found freebayes - /usr/local/bin/freebayes
[06:57:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:57:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:57:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:57:36] Found vcfuniq - /usr/local/bin/vcfuniq
[06:57:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:57:36] Found gzip - /bin/gzip
[06:57:36] Found vt - /usr/local/bin/vt
[06:57:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:57:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:57:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:57:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:57:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:57:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:57:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:57:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:58:06] This is snippy 4.6.0Show full stderr[06:58:06] This is snippy 4.6.0
[06:58:06] Written by Torsten Seemann
[06:58:06] Obtained from https://github.com/tseemann/snippy
[06:58:06] Detected operating system: linux
[06:58:06] Enabling bundled linux tools.
[06:58:06] Found bwa - /usr/local/bin/bwa
[06:58:06] Found bcftools - /usr/local/bin/bcftools
[06:58:06] Found samtools - /usr/local/bin/samtools
[06:58:06] Found java - /usr/local/bin/java
[06:58:06] Found snpEff - /usr/local/bin/snpEff
[06:58:06] Found samclip - /usr/local/bin/samclip
[06:58:06] Found seqtk - /usr/local/bin/seqtk
[06:58:06] Found parallel - /usr/local/bin/parallel
[06:58:06] Found freebayes - /usr/local/bin/freebayes
[06:58:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:06] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:06] Found gzip - /bin/gzip
[06:58:06] Found vt - /usr/local/bin/vt
[06:58:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:58:15] This is snippy 4.6.0Show full stderr[06:58:15] This is snippy 4.6.0
[06:58:15] Written by Torsten Seemann
[06:58:15] Obtained from https://github.com/tseemann/snippy
[06:58:15] Detected operating system: linux
[06:58:15] Enabling bundled linux tools.
[06:58:15] Found bwa - /usr/local/bin/bwa
[06:58:15] Found bcftools - /usr/local/bin/bcftools
[06:58:15] Found samtools - /usr/local/bin/samtools
[06:58:15] Found java - /usr/local/bin/java
[06:58:15] Found snpEff - /usr/local/bin/snpEff
[06:58:15] Found samclip - /usr/local/bin/samclip
[06:58:15] Found seqtk - /usr/local/bin/seqtk
[06:58:15] Found parallel - /usr/local/bin/parallel
[06:58:15] Found freebayes - /usr/local/bin/freebayes
[06:58:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:15] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:16] Found gzip - /bin/gzip
[06:58:16] Found vt - /usr/local/bin/vt
[06:58:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:59:19] This is snippy 4.6.0Show full stderr[06:59:19] This is snippy 4.6.0
[06:59:19] Written by Torsten Seemann
[06:59:19] Obtained from https://github.com/tseemann/snippy
[06:59:19] Detected operating system: linux
[06:59:19] Enabling bundled linux tools.
[06:59:19] Found bwa - /usr/local/bin/bwa
[06:59:19] Found bcftools - /usr/local/bin/bcftools
[06:59:19] Found samtools - /usr/local/bin/samtools
[06:59:19] Found java - /usr/local/bin/java
[06:59:19] Found snpEff - /usr/local/bin/snpEff
[06:59:19] Found samclip - /usr/local/bin/samclip
[06:59:19] Found seqtk - /usr/local/bin/seqtk
[06:59:19] Found parallel - /usr/local/bin/parallel
[06:59:19] Found freebayes - /usr/local/bin/freebayes
[06:59:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:19] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:19] Found gzip - /bin/gzip
[06:59:19] Found vt - /usr/local/bin/vt
[06:59:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:59:40] This is snippy 4.6.0Show full stderr[06:59:40] This is snippy 4.6.0
[06:59:40] Written by Torsten Seemann
[06:59:40] Obtained from https://github.com/tseemann/snippy
[06:59:40] Detected operating system: linux
[06:59:40] Enabling bundled linux tools.
[06:59:40] Found bwa - /usr/local/bin/bwa
[06:59:40] Found bcftools - /usr/local/bin/bcftools
[06:59:40] Found samtools - /usr/local/bin/samtools
[06:59:40] Found java - /usr/local/bin/java
[06:59:40] Found snpEff - /usr/local/bin/snpEff
[06:59:40] Found samclip - /usr/local/bin/samclip
[06:59:40] Found seqtk - /usr/local/bin/seqtk
[06:59:40] Found parallel - /usr/local/bin/parallel
[06:59:40] Found freebayes - /usr/local/bin/freebayes
[06:59:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:40] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:40] Found gzip - /bin/gzip
[06:59:40] Found vt - /usr/local/bin/vt
[06:59:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:59:58] This is snippy 4.6.0Show full stderr[06:59:58] This is snippy 4.6.0
[06:59:58] Written by Torsten Seemann
[06:59:58] Obtained from https://github.com/tseemann/snippy
[06:59:58] Detected operating system: linux
[06:59:58] Enabling bundled linux tools.
[06:59:58] Found bwa - /usr/local/bin/bwa
[06:59:58] Found bcftools - /usr/local/bin/bcftools
[06:59:58] Found samtools - /usr/local/bin/samtools
[06:59:58] Found java - /usr/local/bin/java
[06:59:58] Found snpEff - /usr/local/bin/snpEff
[06:59:58] Found samclip - /usr/local/bin/samclip
[06:59:58] Found seqtk - /usr/local/bin/seqtk
[06:59:58] Found parallel - /usr/local/bin/parallel
[06:59:58] Found freebayes - /usr/local/bin/freebayes
[06:59:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:58] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:58] Found gzip - /bin/gzip
[06:59:58] Found vt - /usr/local/bin/vt
[06:59:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:00:04] This is snippy 4.6.0Show full stderr[07:00:04] This is snippy 4.6.0
[07:00:04] Written by Torsten Seemann
[07:00:04] Obtained from https://github.com/tseemann/snippy
[07:00:04] Detected operating system: linux
[07:00:04] Enabling bundled linux tools.
[07:00:04] Found bwa - /usr/local/bin/bwa
[07:00:04] Found bcftools - /usr/local/bin/bcftools
[07:00:04] Found samtools - /usr/local/bin/samtools
[07:00:04] Found java - /usr/local/bin/java
[07:00:04] Found snpEff - /usr/local/bin/snpEff
[07:00:04] Found samclip - /usr/local/bin/samclip
[07:00:04] Found seqtk - /usr/local/bin/seqtk
[07:00:04] Found parallel - /usr/local/bin/parallel
[07:00:04] Found freebayes - /usr/local/bin/freebayes
[07:00:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:04] Found gzip - /bin/gzip
[07:00:04] Found vt - /usr/local/bin/vt
[07:00:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:00:19] This is snippy 4.6.0Show full stderr[07:00:19] This is snippy 4.6.0
[07:00:19] Written by Torsten Seemann
[07:00:19] Obtained from https://github.com/tseemann/snippy
[07:00:19] Detected operating system: linux
[07:00:19] Enabling bundled linux tools.
[07:00:19] Found bwa - /usr/local/bin/bwa
[07:00:19] Found bcftools - /usr/local/bin/bcftools
[07:00:19] Found samtools - /usr/local/bin/samtools
[07:00:19] Found java - /usr/local/bin/java
[07:00:19] Found snpEff - /usr/local/bin/snpEff
[07:00:19] Found samclip - /usr/local/bin/samclip
[07:00:19] Found seqtk - /usr/local/bin/seqtk
[07:00:19] Found parallel - /usr/local/bin/parallel
[07:00:19] Found freebayes - /usr/local/bin/freebayes
[07:00:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:19] Found gzip - /bin/gzip
[07:00:19] Found vt - /usr/local/bin/vt
[07:00:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:56:58] This is snippy 4.6.0Show full stderr[06:56:58] This is snippy 4.6.0
[06:56:58] Written by Torsten Seemann
[06:56:58] Obtained from https://github.com/tseemann/snippy
[06:56:58] Detected operating system: linux
[06:56:58] Enabling bundled linux tools.
[06:56:58] Found bwa - /usr/local/bin/bwa
[06:56:58] Found bcftools - /usr/local/bin/bcftools
[06:56:58] Found samtools - /usr/local/bin/samtools
[06:56:58] Found java - /usr/local/bin/java
[06:56:58] Found snpEff - /usr/local/bin/snpEff
[06:56:58] Found samclip - /usr/local/bin/samclip
[06:56:58] Found seqtk - /usr/local/bin/seqtk
[06:56:58] Found parallel - /usr/local/bin/parallel
[06:56:58] Found freebayes - /usr/local/bin/freebayes
[06:56:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:56:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:56:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:56:58] Found vcfuniq - /usr/local/bin/vcfuniq
[06:56:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:56:58] Found gzip - /bin/gzip
[06:56:58] Found vt - /usr/local/bin/vt
[06:56:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:56:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:56:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:56:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:56:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:56:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:56:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:56:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:57:14] This is snippy 4.6.0Show full stderr[06:57:14] This is snippy 4.6.0
[06:57:14] Written by Torsten Seemann
[06:57:14] Obtained from https://github.com/tseemann/snippy
[06:57:14] Detected operating system: linux
[06:57:14] Enabling bundled linux tools.
[06:57:14] Found bwa - /usr/local/bin/bwa
[06:57:14] Found bcftools - /usr/local/bin/bcftools
[06:57:14] Found samtools - /usr/local/bin/samtools
[06:57:14] Found java - /usr/local/bin/java
[06:57:14] Found snpEff - /usr/local/bin/snpEff
[06:57:14] Found samclip - /usr/local/bin/samclip
[06:57:14] Found seqtk - /usr/local/bin/seqtk
[06:57:14] Found parallel - /usr/local/bin/parallel
[06:57:14] Found freebayes - /usr/local/bin/freebayes
[06:57:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:57:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:57:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:57:14] Found vcfuniq - /usr/local/bin/vcfuniq
[06:57:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:57:14] Found gzip - /bin/gzip
[06:57:14] Found vt - /usr/local/bin/vt
[06:57:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:57:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:57:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:57:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:57:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:57:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:57:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:57:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:58:43] This is snippy 4.6.0Show full stderr[06:58:43] This is snippy 4.6.0
[06:58:43] Written by Torsten Seemann
[06:58:43] Obtained from https://github.com/tseemann/snippy
[06:58:43] Detected operating system: linux
[06:58:43] Enabling bundled linux tools.
[06:58:43] Found bwa - /usr/local/bin/bwa
[06:58:43] Found bcftools - /usr/local/bin/bcftools
[06:58:43] Found samtools - /usr/local/bin/samtools
[06:58:43] Found java - /usr/local/bin/java
[06:58:43] Found snpEff - /usr/local/bin/snpEff
[06:58:43] Found samclip - /usr/local/bin/samclip
[06:58:43] Found seqtk - /usr/local/bin/seqtk
[06:58:43] Found parallel - /usr/local/bin/parallel
[06:58:43] Found freebayes - /usr/local/bin/freebayes
[06:58:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:43] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:43] Found gzip - /bin/gzip
[06:58:43] Found vt - /usr/local/bin/vt
[06:58:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:59:12] This is snippy 4.6.0Show full stderr[06:59:12] This is snippy 4.6.0
[06:59:12] Written by Torsten Seemann
[06:59:12] Obtained from https://github.com/tseemann/snippy
[06:59:12] Detected operating system: linux
[06:59:12] Enabling bundled linux tools.
[06:59:13] Found bwa - /usr/local/bin/bwa
[06:59:13] Found bcftools - /usr/local/bin/bcftools
[06:59:13] Found samtools - /usr/local/bin/samtools
[06:59:13] Found java - /usr/local/bin/java
[06:59:13] Found snpEff - /usr/local/bin/snpEff
[06:59:13] Found samclip - /usr/local/bin/samclip
[06:59:13] Found seqtk - /usr/local/bin/seqtk
[06:59:13] Found parallel - /usr/local/bin/parallel
[06:59:13] Found freebayes - /usr/local/bin/freebayes
[06:59:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:13] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:13] Found gzip - /bin/gzip
[06:59:13] Found vt - /usr/local/bin/vt
[06:59:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:59:14] This is snippy 4.6.0Show full stderr[06:59:14] This is snippy 4.6.0
[06:59:14] Written by Torsten Seemann
[06:59:14] Obtained from https://github.com/tseemann/snippy
[06:59:14] Detected operating system: linux
[06:59:14] Enabling bundled linux tools.
[06:59:14] Found bwa - /usr/local/bin/bwa
[06:59:14] Found bcftools - /usr/local/bin/bcftools
[06:59:14] Found samtools - /usr/local/bin/samtools
[06:59:14] Found java - /usr/local/bin/java
[06:59:14] Found snpEff - /usr/local/bin/snpEff
[06:59:14] Found samclip - /usr/local/bin/samclip
[06:59:14] Found seqtk - /usr/local/bin/seqtk
[06:59:14] Found parallel - /usr/local/bin/parallel
[06:59:14] Found freebayes - /usr/local/bin/freebayes
[06:59:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:14] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:14] Found gzip - /bin/gzip
[06:59:14] Found vt - /usr/local/bin/vt
[06:59:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:59:49] This is snippy 4.6.0Show full stderr[06:59:49] This is snippy 4.6.0
[06:59:49] Written by Torsten Seemann
[06:59:49] Obtained from https://github.com/tseemann/snippy
[06:59:49] Detected operating system: linux
[06:59:49] Enabling bundled linux tools.
[06:59:49] Found bwa - /usr/local/bin/bwa
[06:59:49] Found bcftools - /usr/local/bin/bcftools
[06:59:49] Found samtools - /usr/local/bin/samtools
[06:59:49] Found java - /usr/local/bin/java
[06:59:49] Found snpEff - /usr/local/bin/snpEff
[06:59:49] Found samclip - /usr/local/bin/samclip
[06:59:49] Found seqtk - /usr/local/bin/seqtk
[06:59:49] Found parallel - /usr/local/bin/parallel
[06:59:49] Found freebayes - /usr/local/bin/freebayes
[06:59:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:49] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:49] Found gzip - /bin/gzip
[06:59:49] Found vt - /usr/local/bin/vt
[06:59:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:00:34] This is snippy 4.6.0Show full stderr[07:00:34] This is snippy 4.6.0
[07:00:34] Written by Torsten Seemann
[07:00:34] Obtained from https://github.com/tseemann/snippy
[07:00:34] Detected operating system: linux
[07:00:34] Enabling bundled linux tools.
[07:00:34] Found bwa - /usr/local/bin/bwa
[07:00:34] Found bcftools - /usr/local/bin/bcftools
[07:00:34] Found samtools - /usr/local/bin/samtools
[07:00:34] Found java - /usr/local/bin/java
[07:00:34] Found snpEff - /usr/local/bin/snpEff
[07:00:34] Found samclip - /usr/local/bin/samclip
[07:00:34] Found seqtk - /usr/local/bin/seqtk
[07:00:34] Found parallel - /usr/local/bin/parallel
[07:00:34] Found freebayes - /usr/local/bin/freebayes
[07:00:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:34] Found gzip - /bin/gzip
[07:00:34] Found vt - /usr/local/bin/vt
[07:00:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:57:47] This is snippy 4.6.0Show full stderr[06:57:47] This is snippy 4.6.0
[06:57:47] Written by Torsten Seemann
[06:57:47] Obtained from https://github.com/tseemann/snippy
[06:57:47] Detected operating system: linux
[06:57:47] Enabling bundled linux tools.
[06:57:47] Found bwa - /usr/local/bin/bwa
[06:57:47] Found bcftools - /usr/local/bin/bcftools
[06:57:47] Found samtools - /usr/local/bin/samtools
[06:57:47] Found java - /usr/local/bin/java
[06:57:47] Found snpEff - /usr/local/bin/snpEff
[06:57:47] Found samclip - /usr/local/bin/samclip
[06:57:47] Found seqtk - /usr/local/bin/seqtk
[06:57:47] Found parallel - /usr/local/bin/parallel
[06:57:47] Found freebayes - /usr/local/bin/freebayes
[06:57:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:57:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:57:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:57:47] Found vcfuniq - /usr/local/bin/vcfuniq
[06:57:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:57:47] Found gzip - /bin/gzip
[06:57:47] Found vt - /usr/local/bin/vt
[06:57:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:57:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:57:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:57:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:57:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:57:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:57:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:57:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:58:18] This is snippy 4.6.0Show full stderr[06:58:18] This is snippy 4.6.0
[06:58:18] Written by Torsten Seemann
[06:58:18] Obtained from https://github.com/tseemann/snippy
[06:58:18] Detected operating system: linux
[06:58:18] Enabling bundled linux tools.
[06:58:18] Found bwa - /usr/local/bin/bwa
[06:58:18] Found bcftools - /usr/local/bin/bcftools
[06:58:18] Found samtools - /usr/local/bin/samtools
[06:58:18] Found java - /usr/local/bin/java
[06:58:18] Found snpEff - /usr/local/bin/snpEff
[06:58:18] Found samclip - /usr/local/bin/samclip
[06:58:18] Found seqtk - /usr/local/bin/seqtk
[06:58:18] Found parallel - /usr/local/bin/parallel
[06:58:18] Found freebayes - /usr/local/bin/freebayes
[06:58:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:18] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:18] Found gzip - /bin/gzip
[06:58:19] Found vt - /usr/local/bin/vt
[06:58:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:58:31] This is snippy 4.6.0Show full stderr[06:58:31] This is snippy 4.6.0
[06:58:31] Written by Torsten Seemann
[06:58:31] Obtained from https://github.com/tseemann/snippy
[06:58:31] Detected operating system: linux
[06:58:31] Enabling bundled linux tools.
[06:58:31] Found bwa - /usr/local/bin/bwa
[06:58:31] Found bcftools - /usr/local/bin/bcftools
[06:58:31] Found samtools - /usr/local/bin/samtools
[06:58:31] Found java - /usr/local/bin/java
[06:58:31] Found snpEff - /usr/local/bin/snpEff
[06:58:31] Found samclip - /usr/local/bin/samclip
[06:58:31] Found seqtk - /usr/local/bin/seqtk
[06:58:31] Found parallel - /usr/local/bin/parallel
[06:58:31] Found freebayes - /usr/local/bin/freebayes
[06:58:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:31] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:31] Found gzip - /bin/gzip
[06:58:31] Found vt - /usr/local/bin/vt
[06:58:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:58:42] This is snippy 4.6.0Show full stderr[06:58:42] This is snippy 4.6.0
[06:58:42] Written by Torsten Seemann
[06:58:42] Obtained from https://github.com/tseemann/snippy
[06:58:42] Detected operating system: linux
[06:58:42] Enabling bundled linux tools.
[06:58:42] Found bwa - /usr/local/bin/bwa
[06:58:43] Found bcftools - /usr/local/bin/bcftools
[06:58:43] Found samtools - /usr/local/bin/samtools
[06:58:43] Found java - /usr/local/bin/java
[06:58:43] Found snpEff - /usr/local/bin/snpEff
[06:58:43] Found samclip - /usr/local/bin/samclip
[06:58:43] Found seqtk - /usr/local/bin/seqtk
[06:58:43] Found parallel - /usr/local/bin/parallel
[06:58:43] Found freebayes - /usr/local/bin/freebayes
[06:58:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:58:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:58:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:58:43] Found vcfuniq - /usr/local/bin/vcfuniq
[06:58:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:58:43] Found gzip - /bin/gzip
[06:58:43] Found vt - /usr/local/bin/vt
[06:58:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:58:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:58:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:58:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:58:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:58:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:58:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:58:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:59:01] This is snippy 4.6.0Show full stderr[06:59:01] This is snippy 4.6.0
[06:59:01] Written by Torsten Seemann
[06:59:01] Obtained from https://github.com/tseemann/snippy
[06:59:01] Detected operating system: linux
[06:59:01] Enabling bundled linux tools.
[06:59:01] Found bwa - /usr/local/bin/bwa
[06:59:01] Found bcftools - /usr/local/bin/bcftools
[06:59:01] Found samtools - /usr/local/bin/samtools
[06:59:01] Found java - /usr/local/bin/java
[06:59:01] Found snpEff - /usr/local/bin/snpEff
[06:59:01] Found samclip - /usr/local/bin/samclip
[06:59:01] Found seqtk - /usr/local/bin/seqtk
[06:59:01] Found parallel - /usr/local/bin/parallel
[06:59:01] Found freebayes - /usr/local/bin/freebayes
[06:59:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:59:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:59:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:59:01] Found vcfuniq - /usr/local/bin/vcfuniq
[06:59:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:59:01] Found gzip - /bin/gzip
[06:59:01] Found vt - /usr/local/bin/vt
[06:59:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:59:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:59:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:59:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:59:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:59:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:59:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:59:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:03:39] This is snippy 4.6.0Show full stderr[08:03:39] This is snippy 4.6.0
[08:03:39] Written by Torsten Seemann
[08:03:39] Obtained from https://github.com/tseemann/snippy
[08:03:39] Detected operating system: linux
[08:03:39] Enabling bundled linux tools.
[08:03:39] Found bwa - /usr/local/bin/bwa
[08:03:39] Found bcftools - /usr/local/bin/bcftools
[08:03:39] Found samtools - /usr/local/bin/samtools
[08:03:39] Found java - /usr/local/bin/java
[08:03:39] Found snpEff - /usr/local/bin/snpEff
[08:03:39] Found samclip - /usr/local/bin/samclip
[08:03:39] Found seqtk - /usr/local/bin/seqtk
[08:03:39] Found parallel - /usr/local/bin/parallel
[08:03:39] Found freebayes - /usr/local/bin/freebayes
[08:03:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:03:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:03:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:03:39] Found vcfuniq - /usr/local/bin/vcfuniq
[08:03:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:03:39] Found gzip - /bin/gzip
[08:03:39] Found vt - /usr/local/bin/vt
[08:03:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:03:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:03:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:03:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:03:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:03:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:03:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:03:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:02:45] This is snippy 4.6.0Show full stderr[07:02:45] This is snippy 4.6.0
[07:02:45] Written by Torsten Seemann
[07:02:45] Obtained from https://github.com/tseemann/snippy
[07:02:45] Detected operating system: linux
[07:02:45] Enabling bundled linux tools.
[07:02:45] Found bwa - /usr/local/bin/bwa
[07:02:45] Found bcftools - /usr/local/bin/bcftools
[07:02:45] Found samtools - /usr/local/bin/samtools
[07:02:45] Found java - /usr/local/bin/java
[07:02:45] Found snpEff - /usr/local/bin/snpEff
[07:02:45] Found samclip - /usr/local/bin/samclip
[07:02:45] Found seqtk - /usr/local/bin/seqtk
[07:02:45] Found parallel - /usr/local/bin/parallel
[07:02:45] Found freebayes - /usr/local/bin/freebayes
[07:02:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:02:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:02:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:02:45] Found vcfuniq - /usr/local/bin/vcfuniq
[07:02:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:02:45] Found gzip - /bin/gzip
[07:02:45] Found vt - /usr/local/bin/vt
[07:02:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:02:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:02:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:02:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:02:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:02:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:02:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:02:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:22] This is snippy 4.6.0Show full stderr[07:03:22] This is snippy 4.6.0
[07:03:22] Written by Torsten Seemann
[07:03:22] Obtained from https://github.com/tseemann/snippy
[07:03:22] Detected operating system: linux
[07:03:22] Enabling bundled linux tools.
[07:03:22] Found bwa - /usr/local/bin/bwa
[07:03:22] Found bcftools - /usr/local/bin/bcftools
[07:03:22] Found samtools - /usr/local/bin/samtools
[07:03:22] Found java - /usr/local/bin/java
[07:03:22] Found snpEff - /usr/local/bin/snpEff
[07:03:22] Found samclip - /usr/local/bin/samclip
[07:03:22] Found seqtk - /usr/local/bin/seqtk
[07:03:22] Found parallel - /usr/local/bin/parallel
[07:03:22] Found freebayes - /usr/local/bin/freebayes
[07:03:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:22] Found gzip - /bin/gzip
[07:03:22] Found vt - /usr/local/bin/vt
[07:03:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:25] This is snippy 4.6.0Show full stderr[07:03:25] This is snippy 4.6.0
[07:03:25] Written by Torsten Seemann
[07:03:25] Obtained from https://github.com/tseemann/snippy
[07:03:25] Detected operating system: linux
[07:03:25] Enabling bundled linux tools.
[07:03:25] Found bwa - /usr/local/bin/bwa
[07:03:25] Found bcftools - /usr/local/bin/bcftools
[07:03:25] Found samtools - /usr/local/bin/samtools
[07:03:25] Found java - /usr/local/bin/java
[07:03:25] Found snpEff - /usr/local/bin/snpEff
[07:03:25] Found samclip - /usr/local/bin/samclip
[07:03:25] Found seqtk - /usr/local/bin/seqtk
[07:03:25] Found parallel - /usr/local/bin/parallel
[07:03:25] Found freebayes - /usr/local/bin/freebayes
[07:03:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:25] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:25] Found gzip - /bin/gzip
[07:03:25] Found vt - /usr/local/bin/vt
[07:03:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:37] This is snippy 4.6.0Show full stderr[07:03:37] This is snippy 4.6.0
[07:03:37] Written by Torsten Seemann
[07:03:37] Obtained from https://github.com/tseemann/snippy
[07:03:37] Detected operating system: linux
[07:03:37] Enabling bundled linux tools.
[07:03:37] Found bwa - /usr/local/bin/bwa
[07:03:37] Found bcftools - /usr/local/bin/bcftools
[07:03:37] Found samtools - /usr/local/bin/samtools
[07:03:37] Found java - /usr/local/bin/java
[07:03:37] Found snpEff - /usr/local/bin/snpEff
[07:03:37] Found samclip - /usr/local/bin/samclip
[07:03:37] Found seqtk - /usr/local/bin/seqtk
[07:03:37] Found parallel - /usr/local/bin/parallel
[07:03:37] Found freebayes - /usr/local/bin/freebayes
[07:03:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:37] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:37] Found gzip - /bin/gzip
[07:03:37] Found vt - /usr/local/bin/vt
[07:03:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:04:07] This is snippy 4.6.0Show full stderr[07:04:07] This is snippy 4.6.0
[07:04:07] Written by Torsten Seemann
[07:04:07] Obtained from https://github.com/tseemann/snippy
[07:04:07] Detected operating system: linux
[07:04:07] Enabling bundled linux tools.
[07:04:07] Found bwa - /usr/local/bin/bwa
[07:04:07] Found bcftools - /usr/local/bin/bcftools
[07:04:07] Found samtools - /usr/local/bin/samtools
[07:04:07] Found java - /usr/local/bin/java
[07:04:07] Found snpEff - /usr/local/bin/snpEff
[07:04:07] Found samclip - /usr/local/bin/samclip
[07:04:07] Found seqtk - /usr/local/bin/seqtk
[07:04:07] Found parallel - /usr/local/bin/parallel
[07:04:07] Found freebayes - /usr/local/bin/freebayes
[07:04:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:07] Found gzip - /bin/gzip
[07:04:07] Found vt - /usr/local/bin/vt
[07:04:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:04:28] This is snippy 4.6.0Show full stderr[07:04:28] This is snippy 4.6.0
[07:04:28] Written by Torsten Seemann
[07:04:28] Obtained from https://github.com/tseemann/snippy
[07:04:28] Detected operating system: linux
[07:04:28] Enabling bundled linux tools.
[07:04:28] Found bwa - /usr/local/bin/bwa
[07:04:28] Found bcftools - /usr/local/bin/bcftools
[07:04:28] Found samtools - /usr/local/bin/samtools
[07:04:28] Found java - /usr/local/bin/java
[07:04:28] Found snpEff - /usr/local/bin/snpEff
[07:04:28] Found samclip - /usr/local/bin/samclip
[07:04:28] Found seqtk - /usr/local/bin/seqtk
[07:04:28] Found parallel - /usr/local/bin/parallel
[07:04:28] Found freebayes - /usr/local/bin/freebayes
[07:04:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:28] Found gzip - /bin/gzip
[07:04:28] Found vt - /usr/local/bin/vt
[07:04:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:03:07] This is snippy 4.6.0Show full stderr[08:03:07] This is snippy 4.6.0
[08:03:07] Written by Torsten Seemann
[08:03:07] Obtained from https://github.com/tseemann/snippy
[08:03:07] Detected operating system: linux
[08:03:07] Enabling bundled linux tools.
[08:03:07] Found bwa - /usr/local/bin/bwa
[08:03:07] Found bcftools - /usr/local/bin/bcftools
[08:03:07] Found samtools - /usr/local/bin/samtools
[08:03:07] Found java - /usr/local/bin/java
[08:03:07] Found snpEff - /usr/local/bin/snpEff
[08:03:07] Found samclip - /usr/local/bin/samclip
[08:03:07] Found seqtk - /usr/local/bin/seqtk
[08:03:07] Found parallel - /usr/local/bin/parallel
[08:03:07] Found freebayes - /usr/local/bin/freebayes
[08:03:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:03:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:03:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:03:07] Found vcfuniq - /usr/local/bin/vcfuniq
[08:03:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:03:07] Found gzip - /bin/gzip
[08:03:07] Found vt - /usr/local/bin/vt
[08:03:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:03:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:03:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:03:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:03:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:03:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:03:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:03:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:01:39] This is snippy 4.6.0Show full stderr[07:01:39] This is snippy 4.6.0
[07:01:39] Written by Torsten Seemann
[07:01:39] Obtained from https://github.com/tseemann/snippy
[07:01:39] Detected operating system: linux
[07:01:39] Enabling bundled linux tools.
[07:01:39] Found bwa - /usr/local/bin/bwa
[07:01:39] Found bcftools - /usr/local/bin/bcftools
[07:01:39] Found samtools - /usr/local/bin/samtools
[07:01:39] Found java - /usr/local/bin/java
[07:01:39] Found snpEff - /usr/local/bin/snpEff
[07:01:39] Found samclip - /usr/local/bin/samclip
[07:01:39] Found seqtk - /usr/local/bin/seqtk
[07:01:39] Found parallel - /usr/local/bin/parallel
[07:01:39] Found freebayes - /usr/local/bin/freebayes
[07:01:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:01:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:01:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:01:39] Found vcfuniq - /usr/local/bin/vcfuniq
[07:01:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:01:39] Found gzip - /bin/gzip
[07:01:39] Found vt - /usr/local/bin/vt
[07:01:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:01:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:01:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:01:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:01:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:01:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:01:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:01:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:13] This is snippy 4.6.0Show full stderr[07:03:13] This is snippy 4.6.0
[07:03:13] Written by Torsten Seemann
[07:03:13] Obtained from https://github.com/tseemann/snippy
[07:03:13] Detected operating system: linux
[07:03:13] Enabling bundled linux tools.
[07:03:13] Found bwa - /usr/local/bin/bwa
[07:03:13] Found bcftools - /usr/local/bin/bcftools
[07:03:13] Found samtools - /usr/local/bin/samtools
[07:03:13] Found java - /usr/local/bin/java
[07:03:13] Found snpEff - /usr/local/bin/snpEff
[07:03:13] Found samclip - /usr/local/bin/samclip
[07:03:13] Found seqtk - /usr/local/bin/seqtk
[07:03:13] Found parallel - /usr/local/bin/parallel
[07:03:13] Found freebayes - /usr/local/bin/freebayes
[07:03:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:13] Found gzip - /bin/gzip
[07:03:13] Found vt - /usr/local/bin/vt
[07:03:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:16] This is snippy 4.6.0Show full stderr[07:03:16] This is snippy 4.6.0
[07:03:16] Written by Torsten Seemann
[07:03:16] Obtained from https://github.com/tseemann/snippy
[07:03:16] Detected operating system: linux
[07:03:16] Enabling bundled linux tools.
[07:03:16] Found bwa - /usr/local/bin/bwa
[07:03:16] Found bcftools - /usr/local/bin/bcftools
[07:03:16] Found samtools - /usr/local/bin/samtools
[07:03:16] Found java - /usr/local/bin/java
[07:03:16] Found snpEff - /usr/local/bin/snpEff
[07:03:16] Found samclip - /usr/local/bin/samclip
[07:03:16] Found seqtk - /usr/local/bin/seqtk
[07:03:16] Found parallel - /usr/local/bin/parallel
[07:03:16] Found freebayes - /usr/local/bin/freebayes
[07:03:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:16] Found gzip - /bin/gzip
[07:03:16] Found vt - /usr/local/bin/vt
[07:03:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:33:36] This is snippy 4.6.0Show full stderr[08:33:36] This is snippy 4.6.0
[08:33:36] Written by Torsten Seemann
[08:33:36] Obtained from https://github.com/tseemann/snippy
[08:33:36] Detected operating system: linux
[08:33:36] Enabling bundled linux tools.
[08:33:36] Found bwa - /usr/local/bin/bwa
[08:33:36] Found bcftools - /usr/local/bin/bcftools
[08:33:36] Found samtools - /usr/local/bin/samtools
[08:33:36] Found java - /usr/local/bin/java
[08:33:36] Found snpEff - /usr/local/bin/snpEff
[08:33:36] Found samclip - /usr/local/bin/samclip
[08:33:36] Found seqtk - /usr/local/bin/seqtk
[08:33:36] Found parallel - /usr/local/bin/parallel
[08:33:36] Found freebayes - /usr/local/bin/freebayes
[08:33:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:33:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:33:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:33:36] Found vcfuniq - /usr/local/bin/vcfuniq
[08:33:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:33:36] Found gzip - /bin/gzip
[08:33:36] Found vt - /usr/local/bin/vt
[08:33:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:33:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:33:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:33:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:33:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:33:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:33:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:33:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:02:07] This is snippy 4.6.0Show full stderr[07:02:07] This is snippy 4.6.0
[07:02:07] Written by Torsten Seemann
[07:02:07] Obtained from https://github.com/tseemann/snippy
[07:02:07] Detected operating system: linux
[07:02:07] Enabling bundled linux tools.
[07:02:07] Found bwa - /usr/local/bin/bwa
[07:02:07] Found bcftools - /usr/local/bin/bcftools
[07:02:07] Found samtools - /usr/local/bin/samtools
[07:02:07] Found java - /usr/local/bin/java
[07:02:07] Found snpEff - /usr/local/bin/snpEff
[07:02:07] Found samclip - /usr/local/bin/samclip
[07:02:07] Found seqtk - /usr/local/bin/seqtk
[07:02:07] Found parallel - /usr/local/bin/parallel
[07:02:07] Found freebayes - /usr/local/bin/freebayes
[07:02:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:02:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:02:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:02:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:02:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:02:07] Found gzip - /bin/gzip
[07:02:07] Found vt - /usr/local/bin/vt
[07:02:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:02:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:02:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:02:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:02:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:02:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:02:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:02:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:02:16] This is snippy 4.6.0Show full stderr[07:02:16] This is snippy 4.6.0
[07:02:16] Written by Torsten Seemann
[07:02:16] Obtained from https://github.com/tseemann/snippy
[07:02:16] Detected operating system: linux
[07:02:16] Enabling bundled linux tools.
[07:02:16] Found bwa - /usr/local/bin/bwa
[07:02:16] Found bcftools - /usr/local/bin/bcftools
[07:02:16] Found samtools - /usr/local/bin/samtools
[07:02:16] Found java - /usr/local/bin/java
[07:02:16] Found snpEff - /usr/local/bin/snpEff
[07:02:16] Found samclip - /usr/local/bin/samclip
[07:02:16] Found seqtk - /usr/local/bin/seqtk
[07:02:16] Found parallel - /usr/local/bin/parallel
[07:02:16] Found freebayes - /usr/local/bin/freebayes
[07:02:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:02:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:02:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:02:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:02:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:02:16] Found gzip - /bin/gzip
[07:02:16] Found vt - /usr/local/bin/vt
[07:02:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:02:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:02:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:02:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:02:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:02:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:02:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:02:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:34:34] This is snippy 4.6.0Show full stderr[08:34:34] This is snippy 4.6.0
[08:34:34] Written by Torsten Seemann
[08:34:34] Obtained from https://github.com/tseemann/snippy
[08:34:34] Detected operating system: linux
[08:34:34] Enabling bundled linux tools.
[08:34:34] Found bwa - /usr/local/bin/bwa
[08:34:34] Found bcftools - /usr/local/bin/bcftools
[08:34:34] Found samtools - /usr/local/bin/samtools
[08:34:34] Found java - /usr/local/bin/java
[08:34:34] Found snpEff - /usr/local/bin/snpEff
[08:34:34] Found samclip - /usr/local/bin/samclip
[08:34:34] Found seqtk - /usr/local/bin/seqtk
[08:34:34] Found parallel - /usr/local/bin/parallel
[08:34:34] Found freebayes - /usr/local/bin/freebayes
[08:34:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:34:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:34:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:34:34] Found vcfuniq - /usr/local/bin/vcfuniq
[08:34:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:34:34] Found gzip - /bin/gzip
[08:34:34] Found vt - /usr/local/bin/vt
[08:34:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:34:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:34:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:34:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:34:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:34:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:34:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:34:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:38:13] This is snippy 4.6.0Show full stderr[07:38:13] This is snippy 4.6.0
[07:38:13] Written by Torsten Seemann
[07:38:13] Obtained from https://github.com/tseemann/snippy
[07:38:13] Detected operating system: linux
[07:38:13] Enabling bundled linux tools.
[07:38:13] Found bwa - /usr/local/bin/bwa
[07:38:13] Found bcftools - /usr/local/bin/bcftools
[07:38:13] Found samtools - /usr/local/bin/samtools
[07:38:13] Found java - /usr/local/bin/java
[07:38:13] Found snpEff - /usr/local/bin/snpEff
[07:38:13] Found samclip - /usr/local/bin/samclip
[07:38:13] Found seqtk - /usr/local/bin/seqtk
[07:38:13] Found parallel - /usr/local/bin/parallel
[07:38:13] Found freebayes - /usr/local/bin/freebayes
[07:38:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:13] Found gzip - /bin/gzip
[07:38:13] Found vt - /usr/local/bin/vt
[07:38:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:00:28] This is snippy 4.6.0Show full stderr[07:00:28] This is snippy 4.6.0
[07:00:28] Written by Torsten Seemann
[07:00:28] Obtained from https://github.com/tseemann/snippy
[07:00:28] Detected operating system: linux
[07:00:28] Enabling bundled linux tools.
[07:00:28] Found bwa - /usr/local/bin/bwa
[07:00:28] Found bcftools - /usr/local/bin/bcftools
[07:00:28] Found samtools - /usr/local/bin/samtools
[07:00:28] Found java - /usr/local/bin/java
[07:00:28] Found snpEff - /usr/local/bin/snpEff
[07:00:28] Found samclip - /usr/local/bin/samclip
[07:00:28] Found seqtk - /usr/local/bin/seqtk
[07:00:28] Found parallel - /usr/local/bin/parallel
[07:00:28] Found freebayes - /usr/local/bin/freebayes
[07:00:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:28] Found gzip - /bin/gzip
[07:00:28] Found vt - /usr/local/bin/vt
[07:00:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:00:43] This is snippy 4.6.0Show full stderr[07:00:43] This is snippy 4.6.0
[07:00:43] Written by Torsten Seemann
[07:00:43] Obtained from https://github.com/tseemann/snippy
[07:00:43] Detected operating system: linux
[07:00:43] Enabling bundled linux tools.
[07:00:43] Found bwa - /usr/local/bin/bwa
[07:00:43] Found bcftools - /usr/local/bin/bcftools
[07:00:43] Found samtools - /usr/local/bin/samtools
[07:00:43] Found java - /usr/local/bin/java
[07:00:43] Found snpEff - /usr/local/bin/snpEff
[07:00:43] Found samclip - /usr/local/bin/samclip
[07:00:43] Found seqtk - /usr/local/bin/seqtk
[07:00:43] Found parallel - /usr/local/bin/parallel
[07:00:43] Found freebayes - /usr/local/bin/freebayes
[07:00:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:00:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:00:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:00:43] Found vcfuniq - /usr/local/bin/vcfuniq
[07:00:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:00:43] Found gzip - /bin/gzip
[07:00:43] Found vt - /usr/local/bin/vt
[07:00:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:00:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:00:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:00:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:00:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:00:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:00:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:00:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:38:56] This is snippy 4.6.0Show full stderr[07:38:56] This is snippy 4.6.0
[07:38:56] Written by Torsten Seemann
[07:38:56] Obtained from https://github.com/tseemann/snippy
[07:38:56] Detected operating system: linux
[07:38:56] Enabling bundled linux tools.
[07:38:56] Found bwa - /usr/local/bin/bwa
[07:38:56] Found bcftools - /usr/local/bin/bcftools
[07:38:56] Found samtools - /usr/local/bin/samtools
[07:38:56] Found java - /usr/local/bin/java
[07:38:56] Found snpEff - /usr/local/bin/snpEff
[07:38:56] Found samclip - /usr/local/bin/samclip
[07:38:56] Found seqtk - /usr/local/bin/seqtk
[07:38:56] Found parallel - /usr/local/bin/parallel
[07:38:56] Found freebayes - /usr/local/bin/freebayes
[07:38:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:56] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:56] Found gzip - /bin/gzip
[07:38:56] Found vt - /usr/local/bin/vt
[07:38:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:01:53] This is snippy 4.6.0Show full stderr[07:01:53] This is snippy 4.6.0
[07:01:53] Written by Torsten Seemann
[07:01:53] Obtained from https://github.com/tseemann/snippy
[07:01:53] Detected operating system: linux
[07:01:53] Enabling bundled linux tools.
[07:01:53] Found bwa - /usr/local/bin/bwa
[07:01:53] Found bcftools - /usr/local/bin/bcftools
[07:01:53] Found samtools - /usr/local/bin/samtools
[07:01:53] Found java - /usr/local/bin/java
[07:01:53] Found snpEff - /usr/local/bin/snpEff
[07:01:53] Found samclip - /usr/local/bin/samclip
[07:01:53] Found seqtk - /usr/local/bin/seqtk
[07:01:53] Found parallel - /usr/local/bin/parallel
[07:01:53] Found freebayes - /usr/local/bin/freebayes
[07:01:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:01:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:01:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:01:53] Found vcfuniq - /usr/local/bin/vcfuniq
[07:01:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:01:53] Found gzip - /bin/gzip
[07:01:53] Found vt - /usr/local/bin/vt
[07:01:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:01:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:01:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:01:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:01:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:01:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:01:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:01:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:02:48] This is snippy 4.6.0Show full stderr[07:02:48] This is snippy 4.6.0
[07:02:48] Written by Torsten Seemann
[07:02:48] Obtained from https://github.com/tseemann/snippy
[07:02:48] Detected operating system: linux
[07:02:48] Enabling bundled linux tools.
[07:02:48] Found bwa - /usr/local/bin/bwa
[07:02:48] Found bcftools - /usr/local/bin/bcftools
[07:02:48] Found samtools - /usr/local/bin/samtools
[07:02:48] Found java - /usr/local/bin/java
[07:02:48] Found snpEff - /usr/local/bin/snpEff
[07:02:48] Found samclip - /usr/local/bin/samclip
[07:02:48] Found seqtk - /usr/local/bin/seqtk
[07:02:48] Found parallel - /usr/local/bin/parallel
[07:02:48] Found freebayes - /usr/local/bin/freebayes
[07:02:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:02:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:02:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:02:48] Found vcfuniq - /usr/local/bin/vcfuniq
[07:02:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:02:48] Found gzip - /bin/gzip
[07:02:48] Found vt - /usr/local/bin/vt
[07:02:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:02:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:02:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:02:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:02:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:02:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:02:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:02:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:00] This is snippy 4.6.0Show full stderr[07:03:00] This is snippy 4.6.0
[07:03:00] Written by Torsten Seemann
[07:03:00] Obtained from https://github.com/tseemann/snippy
[07:03:00] Detected operating system: linux
[07:03:00] Enabling bundled linux tools.
[07:03:00] Found bwa - /usr/local/bin/bwa
[07:03:00] Found bcftools - /usr/local/bin/bcftools
[07:03:00] Found samtools - /usr/local/bin/samtools
[07:03:00] Found java - /usr/local/bin/java
[07:03:00] Found snpEff - /usr/local/bin/snpEff
[07:03:00] Found samclip - /usr/local/bin/samclip
[07:03:00] Found seqtk - /usr/local/bin/seqtk
[07:03:00] Found parallel - /usr/local/bin/parallel
[07:03:00] Found freebayes - /usr/local/bin/freebayes
[07:03:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:00] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:00] Found gzip - /bin/gzip
[07:03:00] Found vt - /usr/local/bin/vt
[07:03:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:04:14] This is snippy 4.6.0Show full stderr[07:04:14] This is snippy 4.6.0
[07:04:14] Written by Torsten Seemann
[07:04:14] Obtained from https://github.com/tseemann/snippy
[07:04:14] Detected operating system: linux
[07:04:14] Enabling bundled linux tools.
[07:04:14] Found bwa - /usr/local/bin/bwa
[07:04:14] Found bcftools - /usr/local/bin/bcftools
[07:04:14] Found samtools - /usr/local/bin/samtools
[07:04:14] Found java - /usr/local/bin/java
[07:04:14] Found snpEff - /usr/local/bin/snpEff
[07:04:14] Found samclip - /usr/local/bin/samclip
[07:04:14] Found seqtk - /usr/local/bin/seqtk
[07:04:14] Found parallel - /usr/local/bin/parallel
[07:04:14] Found freebayes - /usr/local/bin/freebayes
[07:04:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:14] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:14] Found gzip - /bin/gzip
[07:04:14] Found vt - /usr/local/bin/vt
[07:04:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:09:35] This is snippy 4.6.0Show full stderr[08:09:35] This is snippy 4.6.0
[08:09:35] Written by Torsten Seemann
[08:09:35] Obtained from https://github.com/tseemann/snippy
[08:09:35] Detected operating system: linux
[08:09:35] Enabling bundled linux tools.
[08:09:35] Found bwa - /usr/local/bin/bwa
[08:09:35] Found bcftools - /usr/local/bin/bcftools
[08:09:35] Found samtools - /usr/local/bin/samtools
[08:09:35] Found java - /usr/local/bin/java
[08:09:35] Found snpEff - /usr/local/bin/snpEff
[08:09:35] Found samclip - /usr/local/bin/samclip
[08:09:35] Found seqtk - /usr/local/bin/seqtk
[08:09:35] Found parallel - /usr/local/bin/parallel
[08:09:35] Found freebayes - /usr/local/bin/freebayes
[08:09:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:09:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:09:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:09:35] Found vcfuniq - /usr/local/bin/vcfuniq
[08:09:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:09:35] Found gzip - /bin/gzip
[08:09:35] Found vt - /usr/local/bin/vt
[08:09:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:09:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:09:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:09:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:09:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:09:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:09:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:09:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:09:38] This is snippy 4.6.0Show full stderr[08:09:38] This is snippy 4.6.0
[08:09:38] Written by Torsten Seemann
[08:09:38] Obtained from https://github.com/tseemann/snippy
[08:09:38] Detected operating system: linux
[08:09:38] Enabling bundled linux tools.
[08:09:38] Found bwa - /usr/local/bin/bwa
[08:09:38] Found bcftools - /usr/local/bin/bcftools
[08:09:38] Found samtools - /usr/local/bin/samtools
[08:09:38] Found java - /usr/local/bin/java
[08:09:38] Found snpEff - /usr/local/bin/snpEff
[08:09:38] Found samclip - /usr/local/bin/samclip
[08:09:38] Found seqtk - /usr/local/bin/seqtk
[08:09:38] Found parallel - /usr/local/bin/parallel
[08:09:38] Found freebayes - /usr/local/bin/freebayes
[08:09:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:09:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:09:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:09:38] Found vcfuniq - /usr/local/bin/vcfuniq
[08:09:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:09:38] Found gzip - /bin/gzip
[08:09:38] Found vt - /usr/local/bin/vt
[08:09:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:09:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:09:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:09:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:09:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:09:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:09:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:09:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:09:44] This is snippy 4.6.0Show full stderr[08:09:44] This is snippy 4.6.0
[08:09:44] Written by Torsten Seemann
[08:09:44] Obtained from https://github.com/tseemann/snippy
[08:09:44] Detected operating system: linux
[08:09:44] Enabling bundled linux tools.
[08:09:44] Found bwa - /usr/local/bin/bwa
[08:09:44] Found bcftools - /usr/local/bin/bcftools
[08:09:44] Found samtools - /usr/local/bin/samtools
[08:09:44] Found java - /usr/local/bin/java
[08:09:44] Found snpEff - /usr/local/bin/snpEff
[08:09:44] Found samclip - /usr/local/bin/samclip
[08:09:44] Found seqtk - /usr/local/bin/seqtk
[08:09:44] Found parallel - /usr/local/bin/parallel
[08:09:44] Found freebayes - /usr/local/bin/freebayes
[08:09:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:09:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:09:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:09:44] Found vcfuniq - /usr/local/bin/vcfuniq
[08:09:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:09:44] Found gzip - /bin/gzip
[08:09:44] Found vt - /usr/local/bin/vt
[08:09:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:09:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:09:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:09:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:09:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:09:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:09:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:09:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:16:38] This is snippy 4.6.0Show full stderr[08:16:38] This is snippy 4.6.0
[08:16:38] Written by Torsten Seemann
[08:16:38] Obtained from https://github.com/tseemann/snippy
[08:16:38] Detected operating system: linux
[08:16:38] Enabling bundled linux tools.
[08:16:38] Found bwa - /usr/local/bin/bwa
[08:16:38] Found bcftools - /usr/local/bin/bcftools
[08:16:38] Found samtools - /usr/local/bin/samtools
[08:16:38] Found java - /usr/local/bin/java
[08:16:38] Found snpEff - /usr/local/bin/snpEff
[08:16:38] Found samclip - /usr/local/bin/samclip
[08:16:38] Found seqtk - /usr/local/bin/seqtk
[08:16:38] Found parallel - /usr/local/bin/parallel
[08:16:38] Found freebayes - /usr/local/bin/freebayes
[08:16:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:16:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:16:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:16:38] Found vcfuniq - /usr/local/bin/vcfuniq
[08:16:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:16:38] Found gzip - /bin/gzip
[08:16:38] Found vt - /usr/local/bin/vt
[08:16:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:16:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:16:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:16:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:16:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:16:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:16:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:16:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:21:31] This is snippy 4.6.0Show full stderr[08:21:31] This is snippy 4.6.0
[08:21:31] Written by Torsten Seemann
[08:21:31] Obtained from https://github.com/tseemann/snippy
[08:21:31] Detected operating system: linux
[08:21:31] Enabling bundled linux tools.
[08:21:32] Found bwa - /usr/local/bin/bwa
[08:21:32] Found bcftools - /usr/local/bin/bcftools
[08:21:32] Found samtools - /usr/local/bin/samtools
[08:21:32] Found java - /usr/local/bin/java
[08:21:32] Found snpEff - /usr/local/bin/snpEff
[08:21:32] Found samclip - /usr/local/bin/samclip
[08:21:32] Found seqtk - /usr/local/bin/seqtk
[08:21:32] Found parallel - /usr/local/bin/parallel
[08:21:32] Found freebayes - /usr/local/bin/freebayes
[08:21:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:21:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:21:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:21:32] Found vcfuniq - /usr/local/bin/vcfuniq
[08:21:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:21:32] Found gzip - /bin/gzip
[08:21:32] Found vt - /usr/local/bin/vt
[08:21:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:21:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:21:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:21:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:21:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:21:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:21:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:21:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:06:04] This is snippy 4.6.0Show full stderr[07:06:04] This is snippy 4.6.0
[07:06:04] Written by Torsten Seemann
[07:06:04] Obtained from https://github.com/tseemann/snippy
[07:06:04] Detected operating system: linux
[07:06:04] Enabling bundled linux tools.
[07:06:04] Found bwa - /usr/local/bin/bwa
[07:06:04] Found bcftools - /usr/local/bin/bcftools
[07:06:04] Found samtools - /usr/local/bin/samtools
[07:06:04] Found java - /usr/local/bin/java
[07:06:04] Found snpEff - /usr/local/bin/snpEff
[07:06:04] Found samclip - /usr/local/bin/samclip
[07:06:04] Found seqtk - /usr/local/bin/seqtk
[07:06:04] Found parallel - /usr/local/bin/parallel
[07:06:04] Found freebayes - /usr/local/bin/freebayes
[07:06:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:04] Found gzip - /bin/gzip
[07:06:04] Found vt - /usr/local/bin/vt
[07:06:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:28] This is snippy 4.6.0Show full stderr[07:03:28] This is snippy 4.6.0
[07:03:28] Written by Torsten Seemann
[07:03:28] Obtained from https://github.com/tseemann/snippy
[07:03:28] Detected operating system: linux
[07:03:28] Enabling bundled linux tools.
[07:03:28] Found bwa - /usr/local/bin/bwa
[07:03:28] Found bcftools - /usr/local/bin/bcftools
[07:03:28] Found samtools - /usr/local/bin/samtools
[07:03:28] Found java - /usr/local/bin/java
[07:03:28] Found snpEff - /usr/local/bin/snpEff
[07:03:28] Found samclip - /usr/local/bin/samclip
[07:03:28] Found seqtk - /usr/local/bin/seqtk
[07:03:28] Found parallel - /usr/local/bin/parallel
[07:03:28] Found freebayes - /usr/local/bin/freebayes
[07:03:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:28] Found gzip - /bin/gzip
[07:03:28] Found vt - /usr/local/bin/vt
[07:03:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:34] This is snippy 4.6.0Show full stderr[07:03:34] This is snippy 4.6.0
[07:03:34] Written by Torsten Seemann
[07:03:34] Obtained from https://github.com/tseemann/snippy
[07:03:34] Detected operating system: linux
[07:03:34] Enabling bundled linux tools.
[07:03:34] Found bwa - /usr/local/bin/bwa
[07:03:34] Found bcftools - /usr/local/bin/bcftools
[07:03:34] Found samtools - /usr/local/bin/samtools
[07:03:34] Found java - /usr/local/bin/java
[07:03:34] Found snpEff - /usr/local/bin/snpEff
[07:03:34] Found samclip - /usr/local/bin/samclip
[07:03:34] Found seqtk - /usr/local/bin/seqtk
[07:03:34] Found parallel - /usr/local/bin/parallel
[07:03:34] Found freebayes - /usr/local/bin/freebayes
[07:03:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:34] Found gzip - /bin/gzip
[07:03:34] Found vt - /usr/local/bin/vt
[07:03:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:09:25] This is snippy 4.6.0Show full stderr[08:09:25] This is snippy 4.6.0
[08:09:25] Written by Torsten Seemann
[08:09:25] Obtained from https://github.com/tseemann/snippy
[08:09:25] Detected operating system: linux
[08:09:25] Enabling bundled linux tools.
[08:09:25] Found bwa - /usr/local/bin/bwa
[08:09:25] Found bcftools - /usr/local/bin/bcftools
[08:09:25] Found samtools - /usr/local/bin/samtools
[08:09:25] Found java - /usr/local/bin/java
[08:09:25] Found snpEff - /usr/local/bin/snpEff
[08:09:25] Found samclip - /usr/local/bin/samclip
[08:09:25] Found seqtk - /usr/local/bin/seqtk
[08:09:25] Found parallel - /usr/local/bin/parallel
[08:09:25] Found freebayes - /usr/local/bin/freebayes
[08:09:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:09:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:09:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:09:25] Found vcfuniq - /usr/local/bin/vcfuniq
[08:09:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:09:25] Found gzip - /bin/gzip
[08:09:25] Found vt - /usr/local/bin/vt
[08:09:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:09:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:09:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:09:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:09:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:09:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:09:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:09:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:40] This is snippy 4.6.0Show full stderr[07:03:40] This is snippy 4.6.0
[07:03:40] Written by Torsten Seemann
[07:03:40] Obtained from https://github.com/tseemann/snippy
[07:03:40] Detected operating system: linux
[07:03:40] Enabling bundled linux tools.
[07:03:40] Found bwa - /usr/local/bin/bwa
[07:03:40] Found bcftools - /usr/local/bin/bcftools
[07:03:40] Found samtools - /usr/local/bin/samtools
[07:03:40] Found java - /usr/local/bin/java
[07:03:40] Found snpEff - /usr/local/bin/snpEff
[07:03:40] Found samclip - /usr/local/bin/samclip
[07:03:40] Found seqtk - /usr/local/bin/seqtk
[07:03:40] Found parallel - /usr/local/bin/parallel
[07:03:40] Found freebayes - /usr/local/bin/freebayes
[07:03:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:40] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:40] Found gzip - /bin/gzip
[07:03:40] Found vt - /usr/local/bin/vt
[07:03:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:16:35] This is snippy 4.6.0Show full stderr[08:16:35] This is snippy 4.6.0
[08:16:35] Written by Torsten Seemann
[08:16:35] Obtained from https://github.com/tseemann/snippy
[08:16:35] Detected operating system: linux
[08:16:35] Enabling bundled linux tools.
[08:16:35] Found bwa - /usr/local/bin/bwa
[08:16:35] Found bcftools - /usr/local/bin/bcftools
[08:16:35] Found samtools - /usr/local/bin/samtools
[08:16:35] Found java - /usr/local/bin/java
[08:16:35] Found snpEff - /usr/local/bin/snpEff
[08:16:35] Found samclip - /usr/local/bin/samclip
[08:16:35] Found seqtk - /usr/local/bin/seqtk
[08:16:35] Found parallel - /usr/local/bin/parallel
[08:16:35] Found freebayes - /usr/local/bin/freebayes
[08:16:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:16:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:16:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:16:35] Found vcfuniq - /usr/local/bin/vcfuniq
[08:16:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:16:35] Found gzip - /bin/gzip
[08:16:35] Found vt - /usr/local/bin/vt
[08:16:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:16:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:16:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:16:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:16:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:16:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:16:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:16:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:43] This is snippy 4.6.0Show full stderr[07:03:43] This is snippy 4.6.0
[07:03:43] Written by Torsten Seemann
[07:03:43] Obtained from https://github.com/tseemann/snippy
[07:03:43] Detected operating system: linux
[07:03:43] Enabling bundled linux tools.
[07:03:43] Found bwa - /usr/local/bin/bwa
[07:03:43] Found bcftools - /usr/local/bin/bcftools
[07:03:43] Found samtools - /usr/local/bin/samtools
[07:03:43] Found java - /usr/local/bin/java
[07:03:43] Found snpEff - /usr/local/bin/snpEff
[07:03:43] Found samclip - /usr/local/bin/samclip
[07:03:43] Found seqtk - /usr/local/bin/seqtk
[07:03:43] Found parallel - /usr/local/bin/parallel
[07:03:43] Found freebayes - /usr/local/bin/freebayes
[07:03:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:43] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:43] Found gzip - /bin/gzip
[07:03:43] Found vt - /usr/local/bin/vt
[07:03:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:52] This is snippy 4.6.0Show full stderr[07:03:52] This is snippy 4.6.0
[07:03:52] Written by Torsten Seemann
[07:03:52] Obtained from https://github.com/tseemann/snippy
[07:03:52] Detected operating system: linux
[07:03:52] Enabling bundled linux tools.
[07:03:52] Found bwa - /usr/local/bin/bwa
[07:03:52] Found bcftools - /usr/local/bin/bcftools
[07:03:52] Found samtools - /usr/local/bin/samtools
[07:03:52] Found java - /usr/local/bin/java
[07:03:52] Found snpEff - /usr/local/bin/snpEff
[07:03:52] Found samclip - /usr/local/bin/samclip
[07:03:52] Found seqtk - /usr/local/bin/seqtk
[07:03:52] Found parallel - /usr/local/bin/parallel
[07:03:52] Found freebayes - /usr/local/bin/freebayes
[07:03:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:52] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:52] Found gzip - /bin/gzip
[07:03:52] Found vt - /usr/local/bin/vt
[07:03:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:04:01] This is snippy 4.6.0Show full stderr[07:04:01] This is snippy 4.6.0
[07:04:01] Written by Torsten Seemann
[07:04:01] Obtained from https://github.com/tseemann/snippy
[07:04:01] Detected operating system: linux
[07:04:01] Enabling bundled linux tools.
[07:04:01] Found bwa - /usr/local/bin/bwa
[07:04:01] Found bcftools - /usr/local/bin/bcftools
[07:04:01] Found samtools - /usr/local/bin/samtools
[07:04:01] Found java - /usr/local/bin/java
[07:04:01] Found snpEff - /usr/local/bin/snpEff
[07:04:01] Found samclip - /usr/local/bin/samclip
[07:04:01] Found seqtk - /usr/local/bin/seqtk
[07:04:01] Found parallel - /usr/local/bin/parallel
[07:04:01] Found freebayes - /usr/local/bin/freebayes
[07:04:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:01] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:01] Found gzip - /bin/gzip
[07:04:01] Found vt - /usr/local/bin/vt
[07:04:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:04:22] This is snippy 4.6.0Show full stderr[07:04:22] This is snippy 4.6.0
[07:04:22] Written by Torsten Seemann
[07:04:22] Obtained from https://github.com/tseemann/snippy
[07:04:22] Detected operating system: linux
[07:04:22] Enabling bundled linux tools.
[07:04:22] Found bwa - /usr/local/bin/bwa
[07:04:22] Found bcftools - /usr/local/bin/bcftools
[07:04:22] Found samtools - /usr/local/bin/samtools
[07:04:22] Found java - /usr/local/bin/java
[07:04:22] Found snpEff - /usr/local/bin/snpEff
[07:04:22] Found samclip - /usr/local/bin/samclip
[07:04:22] Found seqtk - /usr/local/bin/seqtk
[07:04:22] Found parallel - /usr/local/bin/parallel
[07:04:22] Found freebayes - /usr/local/bin/freebayes
[07:04:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:22] Found gzip - /bin/gzip
[07:04:22] Found vt - /usr/local/bin/vt
[07:04:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:04:37] This is snippy 4.6.0Show full stderr[07:04:37] This is snippy 4.6.0
[07:04:37] Written by Torsten Seemann
[07:04:37] Obtained from https://github.com/tseemann/snippy
[07:04:37] Detected operating system: linux
[07:04:37] Enabling bundled linux tools.
[07:04:37] Found bwa - /usr/local/bin/bwa
[07:04:37] Found bcftools - /usr/local/bin/bcftools
[07:04:37] Found samtools - /usr/local/bin/samtools
[07:04:37] Found java - /usr/local/bin/java
[07:04:37] Found snpEff - /usr/local/bin/snpEff
[07:04:37] Found samclip - /usr/local/bin/samclip
[07:04:37] Found seqtk - /usr/local/bin/seqtk
[07:04:37] Found parallel - /usr/local/bin/parallel
[07:04:37] Found freebayes - /usr/local/bin/freebayes
[07:04:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:37] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:37] Found gzip - /bin/gzip
[07:04:37] Found vt - /usr/local/bin/vt
[07:04:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:04:43] This is snippy 4.6.0Show full stderr[07:04:43] This is snippy 4.6.0
[07:04:43] Written by Torsten Seemann
[07:04:43] Obtained from https://github.com/tseemann/snippy
[07:04:43] Detected operating system: linux
[07:04:43] Enabling bundled linux tools.
[07:04:43] Found bwa - /usr/local/bin/bwa
[07:04:43] Found bcftools - /usr/local/bin/bcftools
[07:04:43] Found samtools - /usr/local/bin/samtools
[07:04:43] Found java - /usr/local/bin/java
[07:04:43] Found snpEff - /usr/local/bin/snpEff
[07:04:43] Found samclip - /usr/local/bin/samclip
[07:04:43] Found seqtk - /usr/local/bin/seqtk
[07:04:43] Found parallel - /usr/local/bin/parallel
[07:04:43] Found freebayes - /usr/local/bin/freebayes
[07:04:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:43] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:43] Found gzip - /bin/gzip
[07:04:43] Found vt - /usr/local/bin/vt
[07:04:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:04:52] This is snippy 4.6.0Show full stderr[07:04:52] This is snippy 4.6.0
[07:04:52] Written by Torsten Seemann
[07:04:52] Obtained from https://github.com/tseemann/snippy
[07:04:52] Detected operating system: linux
[07:04:52] Enabling bundled linux tools.
[07:04:52] Found bwa - /usr/local/bin/bwa
[07:04:52] Found bcftools - /usr/local/bin/bcftools
[07:04:52] Found samtools - /usr/local/bin/samtools
[07:04:52] Found java - /usr/local/bin/java
[07:04:52] Found snpEff - /usr/local/bin/snpEff
[07:04:52] Found samclip - /usr/local/bin/samclip
[07:04:52] Found seqtk - /usr/local/bin/seqtk
[07:04:52] Found parallel - /usr/local/bin/parallel
[07:04:52] Found freebayes - /usr/local/bin/freebayes
[07:04:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:52] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:52] Found gzip - /bin/gzip
[07:04:52] Found vt - /usr/local/bin/vt
[07:04:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:16:51] This is snippy 4.6.0Show full stderr[08:16:51] This is snippy 4.6.0
[08:16:51] Written by Torsten Seemann
[08:16:51] Obtained from https://github.com/tseemann/snippy
[08:16:51] Detected operating system: linux
[08:16:51] Enabling bundled linux tools.
[08:16:51] Found bwa - /usr/local/bin/bwa
[08:16:51] Found bcftools - /usr/local/bin/bcftools
[08:16:51] Found samtools - /usr/local/bin/samtools
[08:16:51] Found java - /usr/local/bin/java
[08:16:51] Found snpEff - /usr/local/bin/snpEff
[08:16:51] Found samclip - /usr/local/bin/samclip
[08:16:51] Found seqtk - /usr/local/bin/seqtk
[08:16:51] Found parallel - /usr/local/bin/parallel
[08:16:51] Found freebayes - /usr/local/bin/freebayes
[08:16:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:16:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:16:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:16:51] Found vcfuniq - /usr/local/bin/vcfuniq
[08:16:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:16:51] Found gzip - /bin/gzip
[08:16:51] Found vt - /usr/local/bin/vt
[08:16:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:16:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:16:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:16:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:16:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:16:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:16:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:16:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:22:52] This is snippy 4.6.0Show full stderr[08:22:52] This is snippy 4.6.0
[08:22:52] Written by Torsten Seemann
[08:22:52] Obtained from https://github.com/tseemann/snippy
[08:22:52] Detected operating system: linux
[08:22:52] Enabling bundled linux tools.
[08:22:52] Found bwa - /usr/local/bin/bwa
[08:22:52] Found bcftools - /usr/local/bin/bcftools
[08:22:52] Found samtools - /usr/local/bin/samtools
[08:22:52] Found java - /usr/local/bin/java
[08:22:52] Found snpEff - /usr/local/bin/snpEff
[08:22:52] Found samclip - /usr/local/bin/samclip
[08:22:52] Found seqtk - /usr/local/bin/seqtk
[08:22:52] Found parallel - /usr/local/bin/parallel
[08:22:52] Found freebayes - /usr/local/bin/freebayes
[08:22:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:22:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:22:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:22:52] Found vcfuniq - /usr/local/bin/vcfuniq
[08:22:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:22:52] Found gzip - /bin/gzip
[08:22:52] Found vt - /usr/local/bin/vt
[08:22:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:22:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:22:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:22:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:22:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:22:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:22:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:22:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:05:04] This is snippy 4.6.0Show full stderr[07:05:04] This is snippy 4.6.0
[07:05:04] Written by Torsten Seemann
[07:05:04] Obtained from https://github.com/tseemann/snippy
[07:05:04] Detected operating system: linux
[07:05:04] Enabling bundled linux tools.
[07:05:04] Found bwa - /usr/local/bin/bwa
[07:05:04] Found bcftools - /usr/local/bin/bcftools
[07:05:04] Found samtools - /usr/local/bin/samtools
[07:05:04] Found java - /usr/local/bin/java
[07:05:04] Found snpEff - /usr/local/bin/snpEff
[07:05:04] Found samclip - /usr/local/bin/samclip
[07:05:04] Found seqtk - /usr/local/bin/seqtk
[07:05:04] Found parallel - /usr/local/bin/parallel
[07:05:04] Found freebayes - /usr/local/bin/freebayes
[07:05:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:04] Found gzip - /bin/gzip
[07:05:04] Found vt - /usr/local/bin/vt
[07:05:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:39:33] This is snippy 4.6.0Show full stderr[08:39:33] This is snippy 4.6.0
[08:39:33] Written by Torsten Seemann
[08:39:33] Obtained from https://github.com/tseemann/snippy
[08:39:33] Detected operating system: linux
[08:39:33] Enabling bundled linux tools.
[08:39:33] Found bwa - /usr/local/bin/bwa
[08:39:33] Found bcftools - /usr/local/bin/bcftools
[08:39:33] Found samtools - /usr/local/bin/samtools
[08:39:33] Found java - /usr/local/bin/java
[08:39:33] Found snpEff - /usr/local/bin/snpEff
[08:39:33] Found samclip - /usr/local/bin/samclip
[08:39:33] Found seqtk - /usr/local/bin/seqtk
[08:39:33] Found parallel - /usr/local/bin/parallel
[08:39:33] Found freebayes - /usr/local/bin/freebayes
[08:39:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:39:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:39:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:39:34] Found vcfuniq - /usr/local/bin/vcfuniq
[08:39:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:39:34] Found gzip - /bin/gzip
[08:39:34] Found vt - /usr/local/bin/vt
[08:39:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:39:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:39:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:39:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:39:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:39:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:39:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:39:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:40:35] This is snippy 4.6.0Show full stderr[08:40:35] This is snippy 4.6.0
[08:40:35] Written by Torsten Seemann
[08:40:35] Obtained from https://github.com/tseemann/snippy
[08:40:35] Detected operating system: linux
[08:40:35] Enabling bundled linux tools.
[08:40:35] Found bwa - /usr/local/bin/bwa
[08:40:35] Found bcftools - /usr/local/bin/bcftools
[08:40:35] Found samtools - /usr/local/bin/samtools
[08:40:35] Found java - /usr/local/bin/java
[08:40:35] Found snpEff - /usr/local/bin/snpEff
[08:40:35] Found samclip - /usr/local/bin/samclip
[08:40:35] Found seqtk - /usr/local/bin/seqtk
[08:40:35] Found parallel - /usr/local/bin/parallel
[08:40:35] Found freebayes - /usr/local/bin/freebayes
[08:40:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:40:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:40:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:40:35] Found vcfuniq - /usr/local/bin/vcfuniq
[08:40:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:40:35] Found gzip - /bin/gzip
[08:40:35] Found vt - /usr/local/bin/vt
[08:40:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:40:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:40:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:40:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:40:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:40:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:40:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:40:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:03] This is snippy 4.6.0Show full stderr[07:03:03] This is snippy 4.6.0
[07:03:03] Written by Torsten Seemann
[07:03:03] Obtained from https://github.com/tseemann/snippy
[07:03:03] Detected operating system: linux
[07:03:03] Enabling bundled linux tools.
[07:03:03] Found bwa - /usr/local/bin/bwa
[07:03:03] Found bcftools - /usr/local/bin/bcftools
[07:03:03] Found samtools - /usr/local/bin/samtools
[07:03:03] Found java - /usr/local/bin/java
[07:03:03] Found snpEff - /usr/local/bin/snpEff
[07:03:03] Found samclip - /usr/local/bin/samclip
[07:03:03] Found seqtk - /usr/local/bin/seqtk
[07:03:03] Found parallel - /usr/local/bin/parallel
[07:03:03] Found freebayes - /usr/local/bin/freebayes
[07:03:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:03] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:03] Found gzip - /bin/gzip
[07:03:03] Found vt - /usr/local/bin/vt
[07:03:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:03:46] This is snippy 4.6.0Show full stderr[07:03:46] This is snippy 4.6.0
[07:03:46] Written by Torsten Seemann
[07:03:46] Obtained from https://github.com/tseemann/snippy
[07:03:46] Detected operating system: linux
[07:03:46] Enabling bundled linux tools.
[07:03:46] Found bwa - /usr/local/bin/bwa
[07:03:46] Found bcftools - /usr/local/bin/bcftools
[07:03:46] Found samtools - /usr/local/bin/samtools
[07:03:46] Found java - /usr/local/bin/java
[07:03:46] Found snpEff - /usr/local/bin/snpEff
[07:03:46] Found samclip - /usr/local/bin/samclip
[07:03:46] Found seqtk - /usr/local/bin/seqtk
[07:03:46] Found parallel - /usr/local/bin/parallel
[07:03:46] Found freebayes - /usr/local/bin/freebayes
[07:03:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:03:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:03:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:03:46] Found vcfuniq - /usr/local/bin/vcfuniq
[07:03:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:03:46] Found gzip - /bin/gzip
[07:03:46] Found vt - /usr/local/bin/vt
[07:03:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:03:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:03:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:03:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:03:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:03:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:03:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:03:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:06:56] This is snippy 4.6.0Show full stderr[07:06:56] This is snippy 4.6.0
[07:06:56] Written by Torsten Seemann
[07:06:56] Obtained from https://github.com/tseemann/snippy
[07:06:56] Detected operating system: linux
[07:06:56] Enabling bundled linux tools.
[07:06:56] Found bwa - /usr/local/bin/bwa
[07:06:56] Found bcftools - /usr/local/bin/bcftools
[07:06:56] Found samtools - /usr/local/bin/samtools
[07:06:56] Found java - /usr/local/bin/java
[07:06:56] Found snpEff - /usr/local/bin/snpEff
[07:06:56] Found samclip - /usr/local/bin/samclip
[07:06:56] Found seqtk - /usr/local/bin/seqtk
[07:06:56] Found parallel - /usr/local/bin/parallel
[07:06:56] Found freebayes - /usr/local/bin/freebayes
[07:06:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:56] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:56] Found gzip - /bin/gzip
[07:06:56] Found vt - /usr/local/bin/vt
[07:06:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:02] This is snippy 4.6.0Show full stderr[07:07:02] This is snippy 4.6.0
[07:07:02] Written by Torsten Seemann
[07:07:02] Obtained from https://github.com/tseemann/snippy
[07:07:02] Detected operating system: linux
[07:07:02] Enabling bundled linux tools.
[07:07:02] Found bwa - /usr/local/bin/bwa
[07:07:02] Found bcftools - /usr/local/bin/bcftools
[07:07:02] Found samtools - /usr/local/bin/samtools
[07:07:02] Found java - /usr/local/bin/java
[07:07:02] Found snpEff - /usr/local/bin/snpEff
[07:07:02] Found samclip - /usr/local/bin/samclip
[07:07:02] Found seqtk - /usr/local/bin/seqtk
[07:07:02] Found parallel - /usr/local/bin/parallel
[07:07:02] Found freebayes - /usr/local/bin/freebayes
[07:07:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:02] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:02] Found gzip - /bin/gzip
[07:07:02] Found vt - /usr/local/bin/vt
[07:07:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:16] This is snippy 4.6.0Show full stderr[07:07:16] This is snippy 4.6.0
[07:07:16] Written by Torsten Seemann
[07:07:16] Obtained from https://github.com/tseemann/snippy
[07:07:16] Detected operating system: linux
[07:07:16] Enabling bundled linux tools.
[07:07:16] Found bwa - /usr/local/bin/bwa
[07:07:16] Found bcftools - /usr/local/bin/bcftools
[07:07:16] Found samtools - /usr/local/bin/samtools
[07:07:16] Found java - /usr/local/bin/java
[07:07:16] Found snpEff - /usr/local/bin/snpEff
[07:07:16] Found samclip - /usr/local/bin/samclip
[07:07:16] Found seqtk - /usr/local/bin/seqtk
[07:07:16] Found parallel - /usr/local/bin/parallel
[07:07:16] Found freebayes - /usr/local/bin/freebayes
[07:07:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:16] Found gzip - /bin/gzip
[07:07:16] Found vt - /usr/local/bin/vt
[07:07:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:31] This is snippy 4.6.0Show full stderr[07:07:31] This is snippy 4.6.0
[07:07:31] Written by Torsten Seemann
[07:07:31] Obtained from https://github.com/tseemann/snippy
[07:07:31] Detected operating system: linux
[07:07:31] Enabling bundled linux tools.
[07:07:31] Found bwa - /usr/local/bin/bwa
[07:07:31] Found bcftools - /usr/local/bin/bcftools
[07:07:31] Found samtools - /usr/local/bin/samtools
[07:07:31] Found java - /usr/local/bin/java
[07:07:31] Found snpEff - /usr/local/bin/snpEff
[07:07:31] Found samclip - /usr/local/bin/samclip
[07:07:31] Found seqtk - /usr/local/bin/seqtk
[07:07:31] Found parallel - /usr/local/bin/parallel
[07:07:31] Found freebayes - /usr/local/bin/freebayes
[07:07:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:31] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:31] Found gzip - /bin/gzip
[07:07:31] Found vt - /usr/local/bin/vt
[07:07:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:56] This is snippy 4.6.0Show full stderr[07:07:56] This is snippy 4.6.0
[07:07:56] Written by Torsten Seemann
[07:07:56] Obtained from https://github.com/tseemann/snippy
[07:07:56] Detected operating system: linux
[07:07:56] Enabling bundled linux tools.
[07:07:56] Found bwa - /usr/local/bin/bwa
[07:07:56] Found bcftools - /usr/local/bin/bcftools
[07:07:56] Found samtools - /usr/local/bin/samtools
[07:07:56] Found java - /usr/local/bin/java
[07:07:56] Found snpEff - /usr/local/bin/snpEff
[07:07:56] Found samclip - /usr/local/bin/samclip
[07:07:56] Found seqtk - /usr/local/bin/seqtk
[07:07:56] Found parallel - /usr/local/bin/parallel
[07:07:56] Found freebayes - /usr/local/bin/freebayes
[07:07:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:56] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:56] Found gzip - /bin/gzip
[07:07:56] Found vt - /usr/local/bin/vt
[07:07:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:08:04] This is snippy 4.6.0Show full stderr[07:08:04] This is snippy 4.6.0
[07:08:04] Written by Torsten Seemann
[07:08:04] Obtained from https://github.com/tseemann/snippy
[07:08:04] Detected operating system: linux
[07:08:04] Enabling bundled linux tools.
[07:08:04] Found bwa - /usr/local/bin/bwa
[07:08:04] Found bcftools - /usr/local/bin/bcftools
[07:08:04] Found samtools - /usr/local/bin/samtools
[07:08:04] Found java - /usr/local/bin/java
[07:08:04] Found snpEff - /usr/local/bin/snpEff
[07:08:04] Found samclip - /usr/local/bin/samclip
[07:08:04] Found seqtk - /usr/local/bin/seqtk
[07:08:04] Found parallel - /usr/local/bin/parallel
[07:08:04] Found freebayes - /usr/local/bin/freebayes
[07:08:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:04] Found gzip - /bin/gzip
[07:08:04] Found vt - /usr/local/bin/vt
[07:08:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:08:25] This is snippy 4.6.0Show full stderr[07:08:25] This is snippy 4.6.0
[07:08:25] Written by Torsten Seemann
[07:08:25] Obtained from https://github.com/tseemann/snippy
[07:08:25] Detected operating system: linux
[07:08:25] Enabling bundled linux tools.
[07:08:25] Found bwa - /usr/local/bin/bwa
[07:08:25] Found bcftools - /usr/local/bin/bcftools
[07:08:25] Found samtools - /usr/local/bin/samtools
[07:08:25] Found java - /usr/local/bin/java
[07:08:25] Found snpEff - /usr/local/bin/snpEff
[07:08:25] Found samclip - /usr/local/bin/samclip
[07:08:25] Found seqtk - /usr/local/bin/seqtk
[07:08:25] Found parallel - /usr/local/bin/parallel
[07:08:25] Found freebayes - /usr/local/bin/freebayes
[07:08:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:25] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:25] Found gzip - /bin/gzip
[07:08:25] Found vt - /usr/local/bin/vt
[07:08:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:22:41] This is snippy 4.6.0Show full stderr[08:22:41] This is snippy 4.6.0
[08:22:41] Written by Torsten Seemann
[08:22:41] Obtained from https://github.com/tseemann/snippy
[08:22:41] Detected operating system: linux
[08:22:41] Enabling bundled linux tools.
[08:22:41] Found bwa - /usr/local/bin/bwa
[08:22:41] Found bcftools - /usr/local/bin/bcftools
[08:22:41] Found samtools - /usr/local/bin/samtools
[08:22:41] Found java - /usr/local/bin/java
[08:22:41] Found snpEff - /usr/local/bin/snpEff
[08:22:41] Found samclip - /usr/local/bin/samclip
[08:22:41] Found seqtk - /usr/local/bin/seqtk
[08:22:41] Found parallel - /usr/local/bin/parallel
[08:22:41] Found freebayes - /usr/local/bin/freebayes
[08:22:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:22:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:22:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:22:41] Found vcfuniq - /usr/local/bin/vcfuniq
[08:22:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:22:41] Found gzip - /bin/gzip
[08:22:41] Found vt - /usr/local/bin/vt
[08:22:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:22:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:22:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:22:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:22:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:22:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:22:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:22:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:08:51] This is snippy 4.6.0Show full stderr[07:08:51] This is snippy 4.6.0
[07:08:51] Written by Torsten Seemann
[07:08:51] Obtained from https://github.com/tseemann/snippy
[07:08:51] Detected operating system: linux
[07:08:51] Enabling bundled linux tools.
[07:08:51] Found bwa - /usr/local/bin/bwa
[07:08:51] Found bcftools - /usr/local/bin/bcftools
[07:08:51] Found samtools - /usr/local/bin/samtools
[07:08:51] Found java - /usr/local/bin/java
[07:08:51] Found snpEff - /usr/local/bin/snpEff
[07:08:51] Found samclip - /usr/local/bin/samclip
[07:08:51] Found seqtk - /usr/local/bin/seqtk
[07:08:51] Found parallel - /usr/local/bin/parallel
[07:08:51] Found freebayes - /usr/local/bin/freebayes
[07:08:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:51] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:51] Found gzip - /bin/gzip
[07:08:51] Found vt - /usr/local/bin/vt
[07:08:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:27:35] This is snippy 4.6.0Show full stderr[08:27:35] This is snippy 4.6.0
[08:27:35] Written by Torsten Seemann
[08:27:35] Obtained from https://github.com/tseemann/snippy
[08:27:35] Detected operating system: linux
[08:27:35] Enabling bundled linux tools.
[08:27:35] Found bwa - /usr/local/bin/bwa
[08:27:35] Found bcftools - /usr/local/bin/bcftools
[08:27:35] Found samtools - /usr/local/bin/samtools
[08:27:35] Found java - /usr/local/bin/java
[08:27:35] Found snpEff - /usr/local/bin/snpEff
[08:27:35] Found samclip - /usr/local/bin/samclip
[08:27:35] Found seqtk - /usr/local/bin/seqtk
[08:27:35] Found parallel - /usr/local/bin/parallel
[08:27:35] Found freebayes - /usr/local/bin/freebayes
[08:27:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:27:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:27:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:27:35] Found vcfuniq - /usr/local/bin/vcfuniq
[08:27:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:27:35] Found gzip - /bin/gzip
[08:27:35] Found vt - /usr/local/bin/vt
[08:27:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:27:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:27:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:27:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:27:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:27:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:27:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:27:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:15] This is snippy 4.6.0Show full stderr[07:44:15] This is snippy 4.6.0
[07:44:15] Written by Torsten Seemann
[07:44:15] Obtained from https://github.com/tseemann/snippy
[07:44:15] Detected operating system: linux
[07:44:15] Enabling bundled linux tools.
[07:44:15] Found bwa - /usr/local/bin/bwa
[07:44:15] Found bcftools - /usr/local/bin/bcftools
[07:44:15] Found samtools - /usr/local/bin/samtools
[07:44:15] Found java - /usr/local/bin/java
[07:44:15] Found snpEff - /usr/local/bin/snpEff
[07:44:15] Found samclip - /usr/local/bin/samclip
[07:44:15] Found seqtk - /usr/local/bin/seqtk
[07:44:15] Found parallel - /usr/local/bin/parallel
[07:44:15] Found freebayes - /usr/local/bin/freebayes
[07:44:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:15] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:15] Found gzip - /bin/gzip
[07:44:15] Found vt - /usr/local/bin/vt
[07:44:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:53] This is snippy 4.6.0Show full stderr[07:44:53] This is snippy 4.6.0
[07:44:53] Written by Torsten Seemann
[07:44:53] Obtained from https://github.com/tseemann/snippy
[07:44:53] Detected operating system: linux
[07:44:53] Enabling bundled linux tools.
[07:44:53] Found bwa - /usr/local/bin/bwa
[07:44:53] Found bcftools - /usr/local/bin/bcftools
[07:44:53] Found samtools - /usr/local/bin/samtools
[07:44:53] Found java - /usr/local/bin/java
[07:44:53] Found snpEff - /usr/local/bin/snpEff
[07:44:53] Found samclip - /usr/local/bin/samclip
[07:44:53] Found seqtk - /usr/local/bin/seqtk
[07:44:53] Found parallel - /usr/local/bin/parallel
[07:44:53] Found freebayes - /usr/local/bin/freebayes
[07:44:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:53] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:53] Found gzip - /bin/gzip
[07:44:53] Found vt - /usr/local/bin/vt
[07:44:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:50:27] This is snippy 4.6.0Show full stderr[07:50:27] This is snippy 4.6.0
[07:50:27] Written by Torsten Seemann
[07:50:27] Obtained from https://github.com/tseemann/snippy
[07:50:27] Detected operating system: linux
[07:50:27] Enabling bundled linux tools.
[07:50:27] Found bwa - /usr/local/bin/bwa
[07:50:27] Found bcftools - /usr/local/bin/bcftools
[07:50:27] Found samtools - /usr/local/bin/samtools
[07:50:27] Found java - /usr/local/bin/java
[07:50:27] Found snpEff - /usr/local/bin/snpEff
[07:50:27] Found samclip - /usr/local/bin/samclip
[07:50:27] Found seqtk - /usr/local/bin/seqtk
[07:50:27] Found parallel - /usr/local/bin/parallel
[07:50:27] Found freebayes - /usr/local/bin/freebayes
[07:50:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:50:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:50:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:50:27] Found vcfuniq - /usr/local/bin/vcfuniq
[07:50:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:50:27] Found gzip - /bin/gzip
[07:50:27] Found vt - /usr/local/bin/vt
[07:50:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:50:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:50:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:50:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:50:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:50:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:50:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:50:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:57:10] This is snippy 4.6.0Show full stderr[07:57:10] This is snippy 4.6.0
[07:57:10] Written by Torsten Seemann
[07:57:10] Obtained from https://github.com/tseemann/snippy
[07:57:10] Detected operating system: linux
[07:57:10] Enabling bundled linux tools.
[07:57:10] Found bwa - /usr/local/bin/bwa
[07:57:10] Found bcftools - /usr/local/bin/bcftools
[07:57:10] Found samtools - /usr/local/bin/samtools
[07:57:10] Found java - /usr/local/bin/java
[07:57:10] Found snpEff - /usr/local/bin/snpEff
[07:57:10] Found samclip - /usr/local/bin/samclip
[07:57:10] Found seqtk - /usr/local/bin/seqtk
[07:57:10] Found parallel - /usr/local/bin/parallel
[07:57:10] Found freebayes - /usr/local/bin/freebayes
[07:57:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:57:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:57:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:57:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:57:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:57:10] Found gzip - /bin/gzip
[07:57:10] Found vt - /usr/local/bin/vt
[07:57:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:57:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:57:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:57:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:57:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:57:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:57:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:57:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:57:12] This is snippy 4.6.0Show full stderr[07:57:12] This is snippy 4.6.0
[07:57:12] Written by Torsten Seemann
[07:57:12] Obtained from https://github.com/tseemann/snippy
[07:57:12] Detected operating system: linux
[07:57:12] Enabling bundled linux tools.
[07:57:12] Found bwa - /usr/local/bin/bwa
[07:57:12] Found bcftools - /usr/local/bin/bcftools
[07:57:12] Found samtools - /usr/local/bin/samtools
[07:57:12] Found java - /usr/local/bin/java
[07:57:12] Found snpEff - /usr/local/bin/snpEff
[07:57:12] Found samclip - /usr/local/bin/samclip
[07:57:12] Found seqtk - /usr/local/bin/seqtk
[07:57:12] Found parallel - /usr/local/bin/parallel
[07:57:12] Found freebayes - /usr/local/bin/freebayes
[07:57:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:57:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:57:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:57:12] Found vcfuniq - /usr/local/bin/vcfuniq
[07:57:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:57:12] Found gzip - /bin/gzip
[07:57:12] Found vt - /usr/local/bin/vt
[07:57:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:57:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:57:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:57:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:57:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:57:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:57:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:57:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:57:27] This is snippy 4.6.0Show full stderr[07:57:27] This is snippy 4.6.0
[07:57:27] Written by Torsten Seemann
[07:57:27] Obtained from https://github.com/tseemann/snippy
[07:57:27] Detected operating system: linux
[07:57:27] Enabling bundled linux tools.
[07:57:27] Found bwa - /usr/local/bin/bwa
[07:57:27] Found bcftools - /usr/local/bin/bcftools
[07:57:27] Found samtools - /usr/local/bin/samtools
[07:57:27] Found java - /usr/local/bin/java
[07:57:27] Found snpEff - /usr/local/bin/snpEff
[07:57:27] Found samclip - /usr/local/bin/samclip
[07:57:27] Found seqtk - /usr/local/bin/seqtk
[07:57:27] Found parallel - /usr/local/bin/parallel
[07:57:27] Found freebayes - /usr/local/bin/freebayes
[07:57:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:57:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:57:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:57:27] Found vcfuniq - /usr/local/bin/vcfuniq
[07:57:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:57:27] Found gzip - /bin/gzip
[07:57:27] Found vt - /usr/local/bin/vt
[07:57:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:57:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:57:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:57:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:57:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:57:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:57:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:57:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:57:30] This is snippy 4.6.0Show full stderr[07:57:30] This is snippy 4.6.0
[07:57:30] Written by Torsten Seemann
[07:57:30] Obtained from https://github.com/tseemann/snippy
[07:57:30] Detected operating system: linux
[07:57:30] Enabling bundled linux tools.
[07:57:30] Found bwa - /usr/local/bin/bwa
[07:57:30] Found bcftools - /usr/local/bin/bcftools
[07:57:30] Found samtools - /usr/local/bin/samtools
[07:57:30] Found java - /usr/local/bin/java
[07:57:30] Found snpEff - /usr/local/bin/snpEff
[07:57:30] Found samclip - /usr/local/bin/samclip
[07:57:30] Found seqtk - /usr/local/bin/seqtk
[07:57:30] Found parallel - /usr/local/bin/parallel
[07:57:30] Found freebayes - /usr/local/bin/freebayes
[07:57:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:57:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:57:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:57:30] Found vcfuniq - /usr/local/bin/vcfuniq
[07:57:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:57:30] Found gzip - /bin/gzip
[07:57:30] Found vt - /usr/local/bin/vt
[07:57:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:57:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:57:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:57:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:57:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:57:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:57:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:57:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:04:49] This is snippy 4.6.0Show full stderr[07:04:49] This is snippy 4.6.0
[07:04:49] Written by Torsten Seemann
[07:04:49] Obtained from https://github.com/tseemann/snippy
[07:04:49] Detected operating system: linux
[07:04:49] Enabling bundled linux tools.
[07:04:49] Found bwa - /usr/local/bin/bwa
[07:04:49] Found bcftools - /usr/local/bin/bcftools
[07:04:49] Found samtools - /usr/local/bin/samtools
[07:04:49] Found java - /usr/local/bin/java
[07:04:49] Found snpEff - /usr/local/bin/snpEff
[07:04:49] Found samclip - /usr/local/bin/samclip
[07:04:49] Found seqtk - /usr/local/bin/seqtk
[07:04:49] Found parallel - /usr/local/bin/parallel
[07:04:49] Found freebayes - /usr/local/bin/freebayes
[07:04:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:49] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:49] Found gzip - /bin/gzip
[07:04:49] Found vt - /usr/local/bin/vt
[07:04:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:04:55] This is snippy 4.6.0Show full stderr[07:04:55] This is snippy 4.6.0
[07:04:55] Written by Torsten Seemann
[07:04:55] Obtained from https://github.com/tseemann/snippy
[07:04:55] Detected operating system: linux
[07:04:55] Enabling bundled linux tools.
[07:04:55] Found bwa - /usr/local/bin/bwa
[07:04:55] Found bcftools - /usr/local/bin/bcftools
[07:04:55] Found samtools - /usr/local/bin/samtools
[07:04:55] Found java - /usr/local/bin/java
[07:04:55] Found snpEff - /usr/local/bin/snpEff
[07:04:55] Found samclip - /usr/local/bin/samclip
[07:04:55] Found seqtk - /usr/local/bin/seqtk
[07:04:55] Found parallel - /usr/local/bin/parallel
[07:04:55] Found freebayes - /usr/local/bin/freebayes
[07:04:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:55] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:55] Found gzip - /bin/gzip
[07:04:55] Found vt - /usr/local/bin/vt
[07:04:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:04:58] This is snippy 4.6.0Show full stderr[07:04:58] This is snippy 4.6.0
[07:04:58] Written by Torsten Seemann
[07:04:58] Obtained from https://github.com/tseemann/snippy
[07:04:58] Detected operating system: linux
[07:04:58] Enabling bundled linux tools.
[07:04:58] Found bwa - /usr/local/bin/bwa
[07:04:58] Found bcftools - /usr/local/bin/bcftools
[07:04:58] Found samtools - /usr/local/bin/samtools
[07:04:58] Found java - /usr/local/bin/java
[07:04:58] Found snpEff - /usr/local/bin/snpEff
[07:04:58] Found samclip - /usr/local/bin/samclip
[07:04:58] Found seqtk - /usr/local/bin/seqtk
[07:04:58] Found parallel - /usr/local/bin/parallel
[07:04:58] Found freebayes - /usr/local/bin/freebayes
[07:04:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:04:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:04:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:04:58] Found vcfuniq - /usr/local/bin/vcfuniq
[07:04:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:04:58] Found gzip - /bin/gzip
[07:04:58] Found vt - /usr/local/bin/vt
[07:04:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:04:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:04:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:04:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:04:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:04:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:04:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:04:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:05:10] This is snippy 4.6.0Show full stderr[07:05:10] This is snippy 4.6.0
[07:05:10] Written by Torsten Seemann
[07:05:10] Obtained from https://github.com/tseemann/snippy
[07:05:10] Detected operating system: linux
[07:05:10] Enabling bundled linux tools.
[07:05:10] Found bwa - /usr/local/bin/bwa
[07:05:10] Found bcftools - /usr/local/bin/bcftools
[07:05:10] Found samtools - /usr/local/bin/samtools
[07:05:10] Found java - /usr/local/bin/java
[07:05:10] Found snpEff - /usr/local/bin/snpEff
[07:05:10] Found samclip - /usr/local/bin/samclip
[07:05:10] Found seqtk - /usr/local/bin/seqtk
[07:05:10] Found parallel - /usr/local/bin/parallel
[07:05:10] Found freebayes - /usr/local/bin/freebayes
[07:05:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:10] Found gzip - /bin/gzip
[07:05:10] Found vt - /usr/local/bin/vt
[07:05:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:05:23] This is snippy 4.6.0Show full stderr[07:05:23] This is snippy 4.6.0
[07:05:23] Written by Torsten Seemann
[07:05:23] Obtained from https://github.com/tseemann/snippy
[07:05:23] Detected operating system: linux
[07:05:23] Enabling bundled linux tools.
[07:05:23] Found bwa - /usr/local/bin/bwa
[07:05:23] Found bcftools - /usr/local/bin/bcftools
[07:05:23] Found samtools - /usr/local/bin/samtools
[07:05:23] Found java - /usr/local/bin/java
[07:05:23] Found snpEff - /usr/local/bin/snpEff
[07:05:23] Found samclip - /usr/local/bin/samclip
[07:05:23] Found seqtk - /usr/local/bin/seqtk
[07:05:23] Found parallel - /usr/local/bin/parallel
[07:05:23] Found freebayes - /usr/local/bin/freebayes
[07:05:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:05:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:05:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:05:23] Found vcfuniq - /usr/local/bin/vcfuniq
[07:05:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:05:23] Found gzip - /bin/gzip
[07:05:23] Found vt - /usr/local/bin/vt
[07:05:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:05:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:05:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:05:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:05:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:05:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:05:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:05:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:06:22] This is snippy 4.6.0Show full stderr[07:06:22] This is snippy 4.6.0
[07:06:22] Written by Torsten Seemann
[07:06:22] Obtained from https://github.com/tseemann/snippy
[07:06:22] Detected operating system: linux
[07:06:22] Enabling bundled linux tools.
[07:06:22] Found bwa - /usr/local/bin/bwa
[07:06:22] Found bcftools - /usr/local/bin/bcftools
[07:06:22] Found samtools - /usr/local/bin/samtools
[07:06:22] Found java - /usr/local/bin/java
[07:06:22] Found snpEff - /usr/local/bin/snpEff
[07:06:22] Found samclip - /usr/local/bin/samclip
[07:06:22] Found seqtk - /usr/local/bin/seqtk
[07:06:22] Found parallel - /usr/local/bin/parallel
[07:06:22] Found freebayes - /usr/local/bin/freebayes
[07:06:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:22] Found gzip - /bin/gzip
[07:06:22] Found vt - /usr/local/bin/vt
[07:06:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:06:50] This is snippy 4.6.0Show full stderr[07:06:50] This is snippy 4.6.0
[07:06:50] Written by Torsten Seemann
[07:06:50] Obtained from https://github.com/tseemann/snippy
[07:06:50] Detected operating system: linux
[07:06:50] Enabling bundled linux tools.
[07:06:50] Found bwa - /usr/local/bin/bwa
[07:06:50] Found bcftools - /usr/local/bin/bcftools
[07:06:50] Found samtools - /usr/local/bin/samtools
[07:06:50] Found java - /usr/local/bin/java
[07:06:50] Found snpEff - /usr/local/bin/snpEff
[07:06:50] Found samclip - /usr/local/bin/samclip
[07:06:50] Found seqtk - /usr/local/bin/seqtk
[07:06:50] Found parallel - /usr/local/bin/parallel
[07:06:50] Found freebayes - /usr/local/bin/freebayes
[07:06:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:50] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:50] Found gzip - /bin/gzip
[07:06:50] Found vt - /usr/local/bin/vt
[07:06:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:47] This is snippy 4.6.0Show full stderr[07:07:47] This is snippy 4.6.0
[07:07:47] Written by Torsten Seemann
[07:07:47] Obtained from https://github.com/tseemann/snippy
[07:07:47] Detected operating system: linux
[07:07:47] Enabling bundled linux tools.
[07:07:47] Found bwa - /usr/local/bin/bwa
[07:07:47] Found bcftools - /usr/local/bin/bcftools
[07:07:47] Found samtools - /usr/local/bin/samtools
[07:07:47] Found java - /usr/local/bin/java
[07:07:47] Found snpEff - /usr/local/bin/snpEff
[07:07:47] Found samclip - /usr/local/bin/samclip
[07:07:47] Found seqtk - /usr/local/bin/seqtk
[07:07:47] Found parallel - /usr/local/bin/parallel
[07:07:47] Found freebayes - /usr/local/bin/freebayes
[07:07:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:47] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:47] Found gzip - /bin/gzip
[07:07:47] Found vt - /usr/local/bin/vt
[07:07:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:53] This is snippy 4.6.0Show full stderr[07:07:53] This is snippy 4.6.0
[07:07:53] Written by Torsten Seemann
[07:07:53] Obtained from https://github.com/tseemann/snippy
[07:07:53] Detected operating system: linux
[07:07:53] Enabling bundled linux tools.
[07:07:53] Found bwa - /usr/local/bin/bwa
[07:07:53] Found bcftools - /usr/local/bin/bcftools
[07:07:53] Found samtools - /usr/local/bin/samtools
[07:07:53] Found java - /usr/local/bin/java
[07:07:53] Found snpEff - /usr/local/bin/snpEff
[07:07:53] Found samclip - /usr/local/bin/samclip
[07:07:53] Found seqtk - /usr/local/bin/seqtk
[07:07:53] Found parallel - /usr/local/bin/parallel
[07:07:53] Found freebayes - /usr/local/bin/freebayes
[07:07:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:53] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:53] Found gzip - /bin/gzip
[07:07:53] Found vt - /usr/local/bin/vt
[07:07:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:08:02] This is snippy 4.6.0Show full stderr[07:08:02] This is snippy 4.6.0
[07:08:02] Written by Torsten Seemann
[07:08:02] Obtained from https://github.com/tseemann/snippy
[07:08:02] Detected operating system: linux
[07:08:02] Enabling bundled linux tools.
[07:08:02] Found bwa - /usr/local/bin/bwa
[07:08:02] Found bcftools - /usr/local/bin/bcftools
[07:08:02] Found samtools - /usr/local/bin/samtools
[07:08:02] Found java - /usr/local/bin/java
[07:08:02] Found snpEff - /usr/local/bin/snpEff
[07:08:02] Found samclip - /usr/local/bin/samclip
[07:08:02] Found seqtk - /usr/local/bin/seqtk
[07:08:02] Found parallel - /usr/local/bin/parallel
[07:08:02] Found freebayes - /usr/local/bin/freebayes
[07:08:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:02] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:02] Found gzip - /bin/gzip
[07:08:02] Found vt - /usr/local/bin/vt
[07:08:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:08:37] This is snippy 4.6.0Show full stderr[07:08:37] This is snippy 4.6.0
[07:08:37] Written by Torsten Seemann
[07:08:37] Obtained from https://github.com/tseemann/snippy
[07:08:37] Detected operating system: linux
[07:08:37] Enabling bundled linux tools.
[07:08:37] Found bwa - /usr/local/bin/bwa
[07:08:37] Found bcftools - /usr/local/bin/bcftools
[07:08:37] Found samtools - /usr/local/bin/samtools
[07:08:37] Found java - /usr/local/bin/java
[07:08:37] Found snpEff - /usr/local/bin/snpEff
[07:08:37] Found samclip - /usr/local/bin/samclip
[07:08:37] Found seqtk - /usr/local/bin/seqtk
[07:08:37] Found parallel - /usr/local/bin/parallel
[07:08:37] Found freebayes - /usr/local/bin/freebayes
[07:08:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:37] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:37] Found gzip - /bin/gzip
[07:08:37] Found vt - /usr/local/bin/vt
[07:08:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:08:48] This is snippy 4.6.0Show full stderr[07:08:48] This is snippy 4.6.0
[07:08:48] Written by Torsten Seemann
[07:08:48] Obtained from https://github.com/tseemann/snippy
[07:08:48] Detected operating system: linux
[07:08:48] Enabling bundled linux tools.
[07:08:48] Found bwa - /usr/local/bin/bwa
[07:08:48] Found bcftools - /usr/local/bin/bcftools
[07:08:48] Found samtools - /usr/local/bin/samtools
[07:08:48] Found java - /usr/local/bin/java
[07:08:48] Found snpEff - /usr/local/bin/snpEff
[07:08:48] Found samclip - /usr/local/bin/samclip
[07:08:48] Found seqtk - /usr/local/bin/seqtk
[07:08:48] Found parallel - /usr/local/bin/parallel
[07:08:48] Found freebayes - /usr/local/bin/freebayes
[07:08:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:48] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:48] Found gzip - /bin/gzip
[07:08:48] Found vt - /usr/local/bin/vt
[07:08:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:09:00] This is snippy 4.6.0Show full stderr[07:09:00] This is snippy 4.6.0
[07:09:00] Written by Torsten Seemann
[07:09:00] Obtained from https://github.com/tseemann/snippy
[07:09:00] Detected operating system: linux
[07:09:00] Enabling bundled linux tools.
[07:09:00] Found bwa - /usr/local/bin/bwa
[07:09:00] Found bcftools - /usr/local/bin/bcftools
[07:09:00] Found samtools - /usr/local/bin/samtools
[07:09:00] Found java - /usr/local/bin/java
[07:09:00] Found snpEff - /usr/local/bin/snpEff
[07:09:00] Found samclip - /usr/local/bin/samclip
[07:09:00] Found seqtk - /usr/local/bin/seqtk
[07:09:00] Found parallel - /usr/local/bin/parallel
[07:09:00] Found freebayes - /usr/local/bin/freebayes
[07:09:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:09:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:09:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:09:00] Found vcfuniq - /usr/local/bin/vcfuniq
[07:09:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:09:00] Found gzip - /bin/gzip
[07:09:00] Found vt - /usr/local/bin/vt
[07:09:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:09:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:09:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:09:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:09:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:09:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:09:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:09:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:15:41] This is snippy 4.6.0Show full stderr[07:15:41] This is snippy 4.6.0
[07:15:41] Written by Torsten Seemann
[07:15:41] Obtained from https://github.com/tseemann/snippy
[07:15:41] Detected operating system: linux
[07:15:41] Enabling bundled linux tools.
[07:15:41] Found bwa - /usr/local/bin/bwa
[07:15:41] Found bcftools - /usr/local/bin/bcftools
[07:15:41] Found samtools - /usr/local/bin/samtools
[07:15:41] Found java - /usr/local/bin/java
[07:15:41] Found snpEff - /usr/local/bin/snpEff
[07:15:41] Found samclip - /usr/local/bin/samclip
[07:15:41] Found seqtk - /usr/local/bin/seqtk
[07:15:41] Found parallel - /usr/local/bin/parallel
[07:15:41] Found freebayes - /usr/local/bin/freebayes
[07:15:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:15:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:15:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:15:41] Found vcfuniq - /usr/local/bin/vcfuniq
[07:15:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:15:41] Found gzip - /bin/gzip
[07:15:41] Found vt - /usr/local/bin/vt
[07:15:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:15:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:15:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:15:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:15:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:15:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:15:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:15:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:41] This is snippy 4.6.0Show full stderr[07:07:41] This is snippy 4.6.0
[07:07:41] Written by Torsten Seemann
[07:07:41] Obtained from https://github.com/tseemann/snippy
[07:07:41] Detected operating system: linux
[07:07:41] Enabling bundled linux tools.
[07:07:41] Found bwa - /usr/local/bin/bwa
[07:07:41] Found bcftools - /usr/local/bin/bcftools
[07:07:41] Found samtools - /usr/local/bin/samtools
[07:07:41] Found java - /usr/local/bin/java
[07:07:41] Found snpEff - /usr/local/bin/snpEff
[07:07:41] Found samclip - /usr/local/bin/samclip
[07:07:41] Found seqtk - /usr/local/bin/seqtk
[07:07:41] Found parallel - /usr/local/bin/parallel
[07:07:41] Found freebayes - /usr/local/bin/freebayes
[07:07:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:41] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:41] Found gzip - /bin/gzip
[07:07:41] Found vt - /usr/local/bin/vt
[07:07:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:08:07] This is snippy 4.6.0Show full stderr[07:08:07] This is snippy 4.6.0
[07:08:07] Written by Torsten Seemann
[07:08:07] Obtained from https://github.com/tseemann/snippy
[07:08:07] Detected operating system: linux
[07:08:07] Enabling bundled linux tools.
[07:08:07] Found bwa - /usr/local/bin/bwa
[07:08:07] Found bcftools - /usr/local/bin/bcftools
[07:08:07] Found samtools - /usr/local/bin/samtools
[07:08:07] Found java - /usr/local/bin/java
[07:08:07] Found snpEff - /usr/local/bin/snpEff
[07:08:07] Found samclip - /usr/local/bin/samclip
[07:08:07] Found seqtk - /usr/local/bin/seqtk
[07:08:07] Found parallel - /usr/local/bin/parallel
[07:08:07] Found freebayes - /usr/local/bin/freebayes
[07:08:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:07] Found gzip - /bin/gzip
[07:08:07] Found vt - /usr/local/bin/vt
[07:08:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:08:10] This is snippy 4.6.0Show full stderr[07:08:10] This is snippy 4.6.0
[07:08:10] Written by Torsten Seemann
[07:08:10] Obtained from https://github.com/tseemann/snippy
[07:08:10] Detected operating system: linux
[07:08:10] Enabling bundled linux tools.
[07:08:10] Found bwa - /usr/local/bin/bwa
[07:08:10] Found bcftools - /usr/local/bin/bcftools
[07:08:10] Found samtools - /usr/local/bin/samtools
[07:08:10] Found java - /usr/local/bin/java
[07:08:10] Found snpEff - /usr/local/bin/snpEff
[07:08:10] Found samclip - /usr/local/bin/samclip
[07:08:10] Found seqtk - /usr/local/bin/seqtk
[07:08:10] Found parallel - /usr/local/bin/parallel
[07:08:10] Found freebayes - /usr/local/bin/freebayes
[07:08:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:10] Found gzip - /bin/gzip
[07:08:10] Found vt - /usr/local/bin/vt
[07:08:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:09:03] This is snippy 4.6.0Show full stderr[07:09:03] This is snippy 4.6.0
[07:09:03] Written by Torsten Seemann
[07:09:03] Obtained from https://github.com/tseemann/snippy
[07:09:03] Detected operating system: linux
[07:09:03] Enabling bundled linux tools.
[07:09:03] Found bwa - /usr/local/bin/bwa
[07:09:03] Found bcftools - /usr/local/bin/bcftools
[07:09:03] Found samtools - /usr/local/bin/samtools
[07:09:03] Found java - /usr/local/bin/java
[07:09:03] Found snpEff - /usr/local/bin/snpEff
[07:09:03] Found samclip - /usr/local/bin/samclip
[07:09:03] Found seqtk - /usr/local/bin/seqtk
[07:09:03] Found parallel - /usr/local/bin/parallel
[07:09:03] Found freebayes - /usr/local/bin/freebayes
[07:09:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:09:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:09:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:09:03] Found vcfuniq - /usr/local/bin/vcfuniq
[07:09:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:09:03] Found gzip - /bin/gzip
[07:09:03] Found vt - /usr/local/bin/vt
[07:09:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:09:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:09:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:09:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:09:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:09:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:09:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:09:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:09:23] This is snippy 4.6.0Show full stderr[07:09:23] This is snippy 4.6.0
[07:09:23] Written by Torsten Seemann
[07:09:23] Obtained from https://github.com/tseemann/snippy
[07:09:23] Detected operating system: linux
[07:09:23] Enabling bundled linux tools.
[07:09:23] Found bwa - /usr/local/bin/bwa
[07:09:23] Found bcftools - /usr/local/bin/bcftools
[07:09:23] Found samtools - /usr/local/bin/samtools
[07:09:23] Found java - /usr/local/bin/java
[07:09:23] Found snpEff - /usr/local/bin/snpEff
[07:09:23] Found samclip - /usr/local/bin/samclip
[07:09:23] Found seqtk - /usr/local/bin/seqtk
[07:09:23] Found parallel - /usr/local/bin/parallel
[07:09:23] Found freebayes - /usr/local/bin/freebayes
[07:09:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:09:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:09:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:09:23] Found vcfuniq - /usr/local/bin/vcfuniq
[07:09:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:09:23] Found gzip - /bin/gzip
[07:09:23] Found vt - /usr/local/bin/vt
[07:09:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:09:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:09:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:09:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:09:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:09:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:09:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:09:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:09:29] This is snippy 4.6.0Show full stderr[07:09:29] This is snippy 4.6.0
[07:09:29] Written by Torsten Seemann
[07:09:29] Obtained from https://github.com/tseemann/snippy
[07:09:29] Detected operating system: linux
[07:09:29] Enabling bundled linux tools.
[07:09:29] Found bwa - /usr/local/bin/bwa
[07:09:29] Found bcftools - /usr/local/bin/bcftools
[07:09:29] Found samtools - /usr/local/bin/samtools
[07:09:29] Found java - /usr/local/bin/java
[07:09:29] Found snpEff - /usr/local/bin/snpEff
[07:09:29] Found samclip - /usr/local/bin/samclip
[07:09:29] Found seqtk - /usr/local/bin/seqtk
[07:09:29] Found parallel - /usr/local/bin/parallel
[07:09:29] Found freebayes - /usr/local/bin/freebayes
[07:09:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:09:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:09:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:09:29] Found vcfuniq - /usr/local/bin/vcfuniq
[07:09:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:09:29] Found gzip - /bin/gzip
[07:09:29] Found vt - /usr/local/bin/vt
[07:09:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:09:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:09:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:09:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:09:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:09:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:09:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:09:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:03:13] This is snippy 4.6.0Show full stderr[08:03:13] This is snippy 4.6.0
[08:03:13] Written by Torsten Seemann
[08:03:13] Obtained from https://github.com/tseemann/snippy
[08:03:13] Detected operating system: linux
[08:03:13] Enabling bundled linux tools.
[08:03:13] Found bwa - /usr/local/bin/bwa
[08:03:13] Found bcftools - /usr/local/bin/bcftools
[08:03:13] Found samtools - /usr/local/bin/samtools
[08:03:13] Found java - /usr/local/bin/java
[08:03:13] Found snpEff - /usr/local/bin/snpEff
[08:03:13] Found samclip - /usr/local/bin/samclip
[08:03:13] Found seqtk - /usr/local/bin/seqtk
[08:03:13] Found parallel - /usr/local/bin/parallel
[08:03:13] Found freebayes - /usr/local/bin/freebayes
[08:03:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:03:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:03:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:03:13] Found vcfuniq - /usr/local/bin/vcfuniq
[08:03:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:03:13] Found gzip - /bin/gzip
[08:03:13] Found vt - /usr/local/bin/vt
[08:03:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:03:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:03:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:03:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:03:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:03:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:03:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:03:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:03:26] This is snippy 4.6.0Show full stderr[08:03:26] This is snippy 4.6.0
[08:03:26] Written by Torsten Seemann
[08:03:26] Obtained from https://github.com/tseemann/snippy
[08:03:26] Detected operating system: linux
[08:03:26] Enabling bundled linux tools.
[08:03:26] Found bwa - /usr/local/bin/bwa
[08:03:26] Found bcftools - /usr/local/bin/bcftools
[08:03:26] Found samtools - /usr/local/bin/samtools
[08:03:26] Found java - /usr/local/bin/java
[08:03:26] Found snpEff - /usr/local/bin/snpEff
[08:03:26] Found samclip - /usr/local/bin/samclip
[08:03:26] Found seqtk - /usr/local/bin/seqtk
[08:03:26] Found parallel - /usr/local/bin/parallel
[08:03:26] Found freebayes - /usr/local/bin/freebayes
[08:03:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:03:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:03:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:03:26] Found vcfuniq - /usr/local/bin/vcfuniq
[08:03:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:03:26] Found gzip - /bin/gzip
[08:03:26] Found vt - /usr/local/bin/vt
[08:03:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:03:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:03:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:03:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:03:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:03:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:03:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:03:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:06:35] This is snippy 4.6.0Show full stderr[07:06:35] This is snippy 4.6.0
[07:06:35] Written by Torsten Seemann
[07:06:35] Obtained from https://github.com/tseemann/snippy
[07:06:35] Detected operating system: linux
[07:06:35] Enabling bundled linux tools.
[07:06:35] Found bwa - /usr/local/bin/bwa
[07:06:35] Found bcftools - /usr/local/bin/bcftools
[07:06:35] Found samtools - /usr/local/bin/samtools
[07:06:35] Found java - /usr/local/bin/java
[07:06:35] Found snpEff - /usr/local/bin/snpEff
[07:06:35] Found samclip - /usr/local/bin/samclip
[07:06:35] Found seqtk - /usr/local/bin/seqtk
[07:06:35] Found parallel - /usr/local/bin/parallel
[07:06:35] Found freebayes - /usr/local/bin/freebayes
[07:06:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:35] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:35] Found gzip - /bin/gzip
[07:06:35] Found vt - /usr/local/bin/vt
[07:06:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:06:41] This is snippy 4.6.0Show full stderr[07:06:41] This is snippy 4.6.0
[07:06:41] Written by Torsten Seemann
[07:06:41] Obtained from https://github.com/tseemann/snippy
[07:06:41] Detected operating system: linux
[07:06:41] Enabling bundled linux tools.
[07:06:41] Found bwa - /usr/local/bin/bwa
[07:06:41] Found bcftools - /usr/local/bin/bcftools
[07:06:41] Found samtools - /usr/local/bin/samtools
[07:06:41] Found java - /usr/local/bin/java
[07:06:41] Found snpEff - /usr/local/bin/snpEff
[07:06:41] Found samclip - /usr/local/bin/samclip
[07:06:41] Found seqtk - /usr/local/bin/seqtk
[07:06:41] Found parallel - /usr/local/bin/parallel
[07:06:41] Found freebayes - /usr/local/bin/freebayes
[07:06:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:41] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:41] Found gzip - /bin/gzip
[07:06:41] Found vt - /usr/local/bin/vt
[07:06:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:25] This is snippy 4.6.0Show full stderr[07:07:25] This is snippy 4.6.0
[07:07:25] Written by Torsten Seemann
[07:07:25] Obtained from https://github.com/tseemann/snippy
[07:07:25] Detected operating system: linux
[07:07:25] Enabling bundled linux tools.
[07:07:25] Found bwa - /usr/local/bin/bwa
[07:07:25] Found bcftools - /usr/local/bin/bcftools
[07:07:25] Found samtools - /usr/local/bin/samtools
[07:07:25] Found java - /usr/local/bin/java
[07:07:25] Found snpEff - /usr/local/bin/snpEff
[07:07:25] Found samclip - /usr/local/bin/samclip
[07:07:25] Found seqtk - /usr/local/bin/seqtk
[07:07:25] Found parallel - /usr/local/bin/parallel
[07:07:25] Found freebayes - /usr/local/bin/freebayes
[07:07:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:25] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:25] Found gzip - /bin/gzip
[07:07:25] Found vt - /usr/local/bin/vt
[07:07:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:50] This is snippy 4.6.0Show full stderr[07:07:50] This is snippy 4.6.0
[07:07:50] Written by Torsten Seemann
[07:07:50] Obtained from https://github.com/tseemann/snippy
[07:07:50] Detected operating system: linux
[07:07:50] Enabling bundled linux tools.
[07:07:50] Found bwa - /usr/local/bin/bwa
[07:07:50] Found bcftools - /usr/local/bin/bcftools
[07:07:50] Found samtools - /usr/local/bin/samtools
[07:07:50] Found java - /usr/local/bin/java
[07:07:50] Found snpEff - /usr/local/bin/snpEff
[07:07:50] Found samclip - /usr/local/bin/samclip
[07:07:50] Found seqtk - /usr/local/bin/seqtk
[07:07:50] Found parallel - /usr/local/bin/parallel
[07:07:50] Found freebayes - /usr/local/bin/freebayes
[07:07:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:50] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:50] Found gzip - /bin/gzip
[07:07:50] Found vt - /usr/local/bin/vt
[07:07:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:08:16] This is snippy 4.6.0Show full stderr[07:08:16] This is snippy 4.6.0
[07:08:16] Written by Torsten Seemann
[07:08:16] Obtained from https://github.com/tseemann/snippy
[07:08:16] Detected operating system: linux
[07:08:16] Enabling bundled linux tools.
[07:08:16] Found bwa - /usr/local/bin/bwa
[07:08:16] Found bcftools - /usr/local/bin/bcftools
[07:08:16] Found samtools - /usr/local/bin/samtools
[07:08:16] Found java - /usr/local/bin/java
[07:08:16] Found snpEff - /usr/local/bin/snpEff
[07:08:16] Found samclip - /usr/local/bin/samclip
[07:08:16] Found seqtk - /usr/local/bin/seqtk
[07:08:16] Found parallel - /usr/local/bin/parallel
[07:08:16] Found freebayes - /usr/local/bin/freebayes
[07:08:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:08:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:08:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:08:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:08:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:08:16] Found gzip - /bin/gzip
[07:08:16] Found vt - /usr/local/bin/vt
[07:08:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:08:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:08:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:08:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:08:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:08:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:08:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:08:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:09:14] This is snippy 4.6.0Show full stderr[07:09:14] This is snippy 4.6.0
[07:09:14] Written by Torsten Seemann
[07:09:14] Obtained from https://github.com/tseemann/snippy
[07:09:14] Detected operating system: linux
[07:09:14] Enabling bundled linux tools.
[07:09:14] Found bwa - /usr/local/bin/bwa
[07:09:14] Found bcftools - /usr/local/bin/bcftools
[07:09:14] Found samtools - /usr/local/bin/samtools
[07:09:14] Found java - /usr/local/bin/java
[07:09:14] Found snpEff - /usr/local/bin/snpEff
[07:09:14] Found samclip - /usr/local/bin/samclip
[07:09:14] Found seqtk - /usr/local/bin/seqtk
[07:09:14] Found parallel - /usr/local/bin/parallel
[07:09:14] Found freebayes - /usr/local/bin/freebayes
[07:09:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:09:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:09:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:09:14] Found vcfuniq - /usr/local/bin/vcfuniq
[07:09:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:09:14] Found gzip - /bin/gzip
[07:09:14] Found vt - /usr/local/bin/vt
[07:09:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:09:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:09:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:09:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:09:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:09:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:09:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:09:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:09:41] This is snippy 4.6.0Show full stderr[07:09:41] This is snippy 4.6.0
[07:09:41] Written by Torsten Seemann
[07:09:41] Obtained from https://github.com/tseemann/snippy
[07:09:41] Detected operating system: linux
[07:09:41] Enabling bundled linux tools.
[07:09:41] Found bwa - /usr/local/bin/bwa
[07:09:41] Found bcftools - /usr/local/bin/bcftools
[07:09:41] Found samtools - /usr/local/bin/samtools
[07:09:41] Found java - /usr/local/bin/java
[07:09:41] Found snpEff - /usr/local/bin/snpEff
[07:09:41] Found samclip - /usr/local/bin/samclip
[07:09:41] Found seqtk - /usr/local/bin/seqtk
[07:09:41] Found parallel - /usr/local/bin/parallel
[07:09:41] Found freebayes - /usr/local/bin/freebayes
[07:09:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:09:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:09:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:09:41] Found vcfuniq - /usr/local/bin/vcfuniq
[07:09:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:09:41] Found gzip - /bin/gzip
[07:09:41] Found vt - /usr/local/bin/vt
[07:09:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:09:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:09:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:09:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:09:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:09:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:09:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:09:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:10:54] This is snippy 4.6.0Show full stderr[07:10:54] This is snippy 4.6.0
[07:10:54] Written by Torsten Seemann
[07:10:54] Obtained from https://github.com/tseemann/snippy
[07:10:54] Detected operating system: linux
[07:10:54] Enabling bundled linux tools.
[07:10:54] Found bwa - /usr/local/bin/bwa
[07:10:54] Found bcftools - /usr/local/bin/bcftools
[07:10:54] Found samtools - /usr/local/bin/samtools
[07:10:54] Found java - /usr/local/bin/java
[07:10:54] Found snpEff - /usr/local/bin/snpEff
[07:10:54] Found samclip - /usr/local/bin/samclip
[07:10:54] Found seqtk - /usr/local/bin/seqtk
[07:10:54] Found parallel - /usr/local/bin/parallel
[07:10:54] Found freebayes - /usr/local/bin/freebayes
[07:10:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:10:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:10:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:10:54] Found vcfuniq - /usr/local/bin/vcfuniq
[07:10:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:10:54] Found gzip - /bin/gzip
[07:10:54] Found vt - /usr/local/bin/vt
[07:10:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:10:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:10:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:10:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:10:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:10:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:10:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:10:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:11:21] This is snippy 4.6.0Show full stderr[07:11:21] This is snippy 4.6.0
[07:11:21] Written by Torsten Seemann
[07:11:21] Obtained from https://github.com/tseemann/snippy
[07:11:21] Detected operating system: linux
[07:11:21] Enabling bundled linux tools.
[07:11:21] Found bwa - /usr/local/bin/bwa
[07:11:21] Found bcftools - /usr/local/bin/bcftools
[07:11:21] Found samtools - /usr/local/bin/samtools
[07:11:21] Found java - /usr/local/bin/java
[07:11:21] Found snpEff - /usr/local/bin/snpEff
[07:11:21] Found samclip - /usr/local/bin/samclip
[07:11:21] Found seqtk - /usr/local/bin/seqtk
[07:11:21] Found parallel - /usr/local/bin/parallel
[07:11:21] Found freebayes - /usr/local/bin/freebayes
[07:11:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:11:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:11:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:11:21] Found vcfuniq - /usr/local/bin/vcfuniq
[07:11:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:11:21] Found gzip - /bin/gzip
[07:11:21] Found vt - /usr/local/bin/vt
[07:11:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:11:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:11:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:11:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:11:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:11:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:11:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:11:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:28:34] This is snippy 4.6.0Show full stderr[08:28:34] This is snippy 4.6.0
[08:28:34] Written by Torsten Seemann
[08:28:34] Obtained from https://github.com/tseemann/snippy
[08:28:34] Detected operating system: linux
[08:28:34] Enabling bundled linux tools.
[08:28:34] Found bwa - /usr/local/bin/bwa
[08:28:34] Found bcftools - /usr/local/bin/bcftools
[08:28:34] Found samtools - /usr/local/bin/samtools
[08:28:34] Found java - /usr/local/bin/java
[08:28:34] Found snpEff - /usr/local/bin/snpEff
[08:28:34] Found samclip - /usr/local/bin/samclip
[08:28:34] Found seqtk - /usr/local/bin/seqtk
[08:28:34] Found parallel - /usr/local/bin/parallel
[08:28:34] Found freebayes - /usr/local/bin/freebayes
[08:28:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:28:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:28:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:28:34] Found vcfuniq - /usr/local/bin/vcfuniq
[08:28:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:28:34] Found gzip - /bin/gzip
[08:28:34] Found vt - /usr/local/bin/vt
[08:28:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:28:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:28:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:28:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:28:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:28:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:28:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:28:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:33:31] This is snippy 4.6.0Show full stderr[08:33:31] This is snippy 4.6.0
[08:33:31] Written by Torsten Seemann
[08:33:31] Obtained from https://github.com/tseemann/snippy
[08:33:31] Detected operating system: linux
[08:33:31] Enabling bundled linux tools.
[08:33:31] Found bwa - /usr/local/bin/bwa
[08:33:31] Found bcftools - /usr/local/bin/bcftools
[08:33:31] Found samtools - /usr/local/bin/samtools
[08:33:31] Found java - /usr/local/bin/java
[08:33:31] Found snpEff - /usr/local/bin/snpEff
[08:33:31] Found samclip - /usr/local/bin/samclip
[08:33:31] Found seqtk - /usr/local/bin/seqtk
[08:33:31] Found parallel - /usr/local/bin/parallel
[08:33:31] Found freebayes - /usr/local/bin/freebayes
[08:33:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:33:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:33:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:33:31] Found vcfuniq - /usr/local/bin/vcfuniq
[08:33:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:33:31] Found gzip - /bin/gzip
[08:33:31] Found vt - /usr/local/bin/vt
[08:33:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:33:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:33:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:33:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:33:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:33:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:33:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:33:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:12:35] This is snippy 4.6.0Show full stderr[07:12:35] This is snippy 4.6.0
[07:12:35] Written by Torsten Seemann
[07:12:35] Obtained from https://github.com/tseemann/snippy
[07:12:35] Detected operating system: linux
[07:12:35] Enabling bundled linux tools.
[07:12:35] Found bwa - /usr/local/bin/bwa
[07:12:35] Found bcftools - /usr/local/bin/bcftools
[07:12:35] Found samtools - /usr/local/bin/samtools
[07:12:35] Found java - /usr/local/bin/java
[07:12:35] Found snpEff - /usr/local/bin/snpEff
[07:12:35] Found samclip - /usr/local/bin/samclip
[07:12:35] Found seqtk - /usr/local/bin/seqtk
[07:12:35] Found parallel - /usr/local/bin/parallel
[07:12:35] Found freebayes - /usr/local/bin/freebayes
[07:12:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:12:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:12:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:12:35] Found vcfuniq - /usr/local/bin/vcfuniq
[07:12:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:12:35] Found gzip - /bin/gzip
[07:12:36] Found vt - /usr/local/bin/vt
[07:12:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:12:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:12:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:12:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:12:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:12:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:12:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:12:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:13:14] This is snippy 4.6.0Show full stderr[07:13:14] This is snippy 4.6.0
[07:13:14] Written by Torsten Seemann
[07:13:14] Obtained from https://github.com/tseemann/snippy
[07:13:14] Detected operating system: linux
[07:13:14] Enabling bundled linux tools.
[07:13:14] Found bwa - /usr/local/bin/bwa
[07:13:14] Found bcftools - /usr/local/bin/bcftools
[07:13:14] Found samtools - /usr/local/bin/samtools
[07:13:14] Found java - /usr/local/bin/java
[07:13:14] Found snpEff - /usr/local/bin/snpEff
[07:13:14] Found samclip - /usr/local/bin/samclip
[07:13:14] Found seqtk - /usr/local/bin/seqtk
[07:13:14] Found parallel - /usr/local/bin/parallel
[07:13:14] Found freebayes - /usr/local/bin/freebayes
[07:13:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:13:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:13:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:13:14] Found vcfuniq - /usr/local/bin/vcfuniq
[07:13:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:13:14] Found gzip - /bin/gzip
[07:13:14] Found vt - /usr/local/bin/vt
[07:13:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:13:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:13:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:13:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:13:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:13:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:13:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:13:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:13:02] This is snippy 4.6.0Show full stderr[07:13:02] This is snippy 4.6.0
[07:13:02] Written by Torsten Seemann
[07:13:02] Obtained from https://github.com/tseemann/snippy
[07:13:02] Detected operating system: linux
[07:13:02] Enabling bundled linux tools.
[07:13:02] Found bwa - /usr/local/bin/bwa
[07:13:02] Found bcftools - /usr/local/bin/bcftools
[07:13:02] Found samtools - /usr/local/bin/samtools
[07:13:02] Found java - /usr/local/bin/java
[07:13:02] Found snpEff - /usr/local/bin/snpEff
[07:13:02] Found samclip - /usr/local/bin/samclip
[07:13:02] Found seqtk - /usr/local/bin/seqtk
[07:13:02] Found parallel - /usr/local/bin/parallel
[07:13:02] Found freebayes - /usr/local/bin/freebayes
[07:13:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:13:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:13:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:13:02] Found vcfuniq - /usr/local/bin/vcfuniq
[07:13:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:13:02] Found gzip - /bin/gzip
[07:13:02] Found vt - /usr/local/bin/vt
[07:13:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:13:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:13:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:13:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:13:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:13:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:13:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:13:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:13:01] This is snippy 4.6.0Show full stderr[07:13:01] This is snippy 4.6.0
[07:13:01] Written by Torsten Seemann
[07:13:01] Obtained from https://github.com/tseemann/snippy
[07:13:01] Detected operating system: linux
[07:13:01] Enabling bundled linux tools.
[07:13:01] Found bwa - /usr/local/bin/bwa
[07:13:01] Found bcftools - /usr/local/bin/bcftools
[07:13:01] Found samtools - /usr/local/bin/samtools
[07:13:01] Found java - /usr/local/bin/java
[07:13:01] Found snpEff - /usr/local/bin/snpEff
[07:13:01] Found samclip - /usr/local/bin/samclip
[07:13:01] Found seqtk - /usr/local/bin/seqtk
[07:13:01] Found parallel - /usr/local/bin/parallel
[07:13:01] Found freebayes - /usr/local/bin/freebayes
[07:13:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:13:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:13:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:13:02] Found vcfuniq - /usr/local/bin/vcfuniq
[07:13:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:13:02] Found gzip - /bin/gzip
[07:13:02] Found vt - /usr/local/bin/vt
[07:13:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:13:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:13:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:13:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:13:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:13:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:13:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:13:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:15:55] This is snippy 4.6.0Show full stderr[07:15:55] This is snippy 4.6.0
[07:15:55] Written by Torsten Seemann
[07:15:55] Obtained from https://github.com/tseemann/snippy
[07:15:55] Detected operating system: linux
[07:15:55] Enabling bundled linux tools.
[07:15:55] Found bwa - /usr/local/bin/bwa
[07:15:55] Found bcftools - /usr/local/bin/bcftools
[07:15:55] Found samtools - /usr/local/bin/samtools
[07:15:55] Found java - /usr/local/bin/java
[07:15:55] Found snpEff - /usr/local/bin/snpEff
[07:15:55] Found samclip - /usr/local/bin/samclip
[07:15:55] Found seqtk - /usr/local/bin/seqtk
[07:15:55] Found parallel - /usr/local/bin/parallel
[07:15:55] Found freebayes - /usr/local/bin/freebayes
[07:15:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:15:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:15:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:15:55] Found vcfuniq - /usr/local/bin/vcfuniq
[07:15:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:15:55] Found gzip - /bin/gzip
[07:15:55] Found vt - /usr/local/bin/vt
[07:15:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:15:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:15:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:15:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:15:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:15:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:15:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:15:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:14:57] This is snippy 4.6.0Show full stderr[07:14:57] This is snippy 4.6.0
[07:14:57] Written by Torsten Seemann
[07:14:57] Obtained from https://github.com/tseemann/snippy
[07:14:57] Detected operating system: linux
[07:14:57] Enabling bundled linux tools.
[07:14:57] Found bwa - /usr/local/bin/bwa
[07:14:57] Found bcftools - /usr/local/bin/bcftools
[07:14:57] Found samtools - /usr/local/bin/samtools
[07:14:57] Found java - /usr/local/bin/java
[07:14:57] Found snpEff - /usr/local/bin/snpEff
[07:14:57] Found samclip - /usr/local/bin/samclip
[07:14:57] Found seqtk - /usr/local/bin/seqtk
[07:14:57] Found parallel - /usr/local/bin/parallel
[07:14:57] Found freebayes - /usr/local/bin/freebayes
[07:14:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:14:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:14:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:14:57] Found vcfuniq - /usr/local/bin/vcfuniq
[07:14:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:14:57] Found gzip - /bin/gzip
[07:14:57] Found vt - /usr/local/bin/vt
[07:14:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:14:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:14:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:14:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:14:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:14:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:14:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:14:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:15:27] This is snippy 4.6.0Show full stderr[07:15:27] This is snippy 4.6.0
[07:15:27] Written by Torsten Seemann
[07:15:27] Obtained from https://github.com/tseemann/snippy
[07:15:27] Detected operating system: linux
[07:15:27] Enabling bundled linux tools.
[07:15:27] Found bwa - /usr/local/bin/bwa
[07:15:27] Found bcftools - /usr/local/bin/bcftools
[07:15:27] Found samtools - /usr/local/bin/samtools
[07:15:27] Found java - /usr/local/bin/java
[07:15:27] Found snpEff - /usr/local/bin/snpEff
[07:15:27] Found samclip - /usr/local/bin/samclip
[07:15:27] Found seqtk - /usr/local/bin/seqtk
[07:15:27] Found parallel - /usr/local/bin/parallel
[07:15:27] Found freebayes - /usr/local/bin/freebayes
[07:15:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:15:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:15:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:15:27] Found vcfuniq - /usr/local/bin/vcfuniq
[07:15:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:15:27] Found gzip - /bin/gzip
[07:15:27] Found vt - /usr/local/bin/vt
[07:15:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:15:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:15:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:15:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:15:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:15:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:15:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:15:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:15:38] This is snippy 4.6.0Show full stderr[07:15:38] This is snippy 4.6.0
[07:15:38] Written by Torsten Seemann
[07:15:38] Obtained from https://github.com/tseemann/snippy
[07:15:38] Detected operating system: linux
[07:15:38] Enabling bundled linux tools.
[07:15:38] Found bwa - /usr/local/bin/bwa
[07:15:38] Found bcftools - /usr/local/bin/bcftools
[07:15:38] Found samtools - /usr/local/bin/samtools
[07:15:38] Found java - /usr/local/bin/java
[07:15:38] Found snpEff - /usr/local/bin/snpEff
[07:15:38] Found samclip - /usr/local/bin/samclip
[07:15:38] Found seqtk - /usr/local/bin/seqtk
[07:15:38] Found parallel - /usr/local/bin/parallel
[07:15:38] Found freebayes - /usr/local/bin/freebayes
[07:15:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:15:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:15:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:15:38] Found vcfuniq - /usr/local/bin/vcfuniq
[07:15:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:15:38] Found gzip - /bin/gzip
[07:15:38] Found vt - /usr/local/bin/vt
[07:15:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:15:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:15:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:15:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:15:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:15:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:15:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:15:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:15:52] This is snippy 4.6.0Show full stderr[07:15:52] This is snippy 4.6.0
[07:15:52] Written by Torsten Seemann
[07:15:52] Obtained from https://github.com/tseemann/snippy
[07:15:52] Detected operating system: linux
[07:15:52] Enabling bundled linux tools.
[07:15:52] Found bwa - /usr/local/bin/bwa
[07:15:52] Found bcftools - /usr/local/bin/bcftools
[07:15:52] Found samtools - /usr/local/bin/samtools
[07:15:52] Found java - /usr/local/bin/java
[07:15:52] Found snpEff - /usr/local/bin/snpEff
[07:15:52] Found samclip - /usr/local/bin/samclip
[07:15:52] Found seqtk - /usr/local/bin/seqtk
[07:15:52] Found parallel - /usr/local/bin/parallel
[07:15:52] Found freebayes - /usr/local/bin/freebayes
[07:15:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:15:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:15:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:15:52] Found vcfuniq - /usr/local/bin/vcfuniq
[07:15:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:15:52] Found gzip - /bin/gzip
[07:15:52] Found vt - /usr/local/bin/vt
[07:15:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:15:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:15:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:15:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:15:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:15:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:15:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:15:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:45:37] This is snippy 4.6.0Show full stderr[08:45:37] This is snippy 4.6.0
[08:45:37] Written by Torsten Seemann
[08:45:37] Obtained from https://github.com/tseemann/snippy
[08:45:37] Detected operating system: linux
[08:45:37] Enabling bundled linux tools.
[08:45:37] Found bwa - /usr/local/bin/bwa
[08:45:37] Found bcftools - /usr/local/bin/bcftools
[08:45:37] Found samtools - /usr/local/bin/samtools
[08:45:37] Found java - /usr/local/bin/java
[08:45:37] Found snpEff - /usr/local/bin/snpEff
[08:45:37] Found samclip - /usr/local/bin/samclip
[08:45:37] Found seqtk - /usr/local/bin/seqtk
[08:45:37] Found parallel - /usr/local/bin/parallel
[08:45:37] Found freebayes - /usr/local/bin/freebayes
[08:45:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:45:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:45:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:45:37] Found vcfuniq - /usr/local/bin/vcfuniq
[08:45:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:45:37] Found gzip - /bin/gzip
[08:45:37] Found vt - /usr/local/bin/vt
[08:45:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:45:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:45:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:45:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:45:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:45:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:45:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:45:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:16:10] This is snippy 4.6.0Show full stderr[07:16:10] This is snippy 4.6.0
[07:16:10] Written by Torsten Seemann
[07:16:10] Obtained from https://github.com/tseemann/snippy
[07:16:10] Detected operating system: linux
[07:16:10] Enabling bundled linux tools.
[07:16:10] Found bwa - /usr/local/bin/bwa
[07:16:10] Found bcftools - /usr/local/bin/bcftools
[07:16:10] Found samtools - /usr/local/bin/samtools
[07:16:10] Found java - /usr/local/bin/java
[07:16:10] Found snpEff - /usr/local/bin/snpEff
[07:16:10] Found samclip - /usr/local/bin/samclip
[07:16:10] Found seqtk - /usr/local/bin/seqtk
[07:16:10] Found parallel - /usr/local/bin/parallel
[07:16:10] Found freebayes - /usr/local/bin/freebayes
[07:16:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:16:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:16:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:16:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:16:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:16:10] Found gzip - /bin/gzip
[07:16:10] Found vt - /usr/local/bin/vt
[07:16:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:16:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:16:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:16:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:16:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:16:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:16:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:16:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:03:33] This is snippy 4.6.0Show full stderr[08:03:33] This is snippy 4.6.0
[08:03:33] Written by Torsten Seemann
[08:03:33] Obtained from https://github.com/tseemann/snippy
[08:03:33] Detected operating system: linux
[08:03:33] Enabling bundled linux tools.
[08:03:33] Found bwa - /usr/local/bin/bwa
[08:03:33] Found bcftools - /usr/local/bin/bcftools
[08:03:33] Found samtools - /usr/local/bin/samtools
[08:03:33] Found java - /usr/local/bin/java
[08:03:33] Found snpEff - /usr/local/bin/snpEff
[08:03:33] Found samclip - /usr/local/bin/samclip
[08:03:33] Found seqtk - /usr/local/bin/seqtk
[08:03:33] Found parallel - /usr/local/bin/parallel
[08:03:33] Found freebayes - /usr/local/bin/freebayes
[08:03:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:03:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:03:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:03:33] Found vcfuniq - /usr/local/bin/vcfuniq
[08:03:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:03:33] Found gzip - /bin/gzip
[08:03:33] Found vt - /usr/local/bin/vt
[08:03:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:03:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:03:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:03:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:03:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:03:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:03:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:03:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:15:13] This is snippy 4.6.0Show full stderr[07:15:13] This is snippy 4.6.0
[07:15:13] Written by Torsten Seemann
[07:15:13] Obtained from https://github.com/tseemann/snippy
[07:15:13] Detected operating system: linux
[07:15:13] Enabling bundled linux tools.
[07:15:13] Found bwa - /usr/local/bin/bwa
[07:15:13] Found bcftools - /usr/local/bin/bcftools
[07:15:13] Found samtools - /usr/local/bin/samtools
[07:15:13] Found java - /usr/local/bin/java
[07:15:13] Found snpEff - /usr/local/bin/snpEff
[07:15:13] Found samclip - /usr/local/bin/samclip
[07:15:13] Found seqtk - /usr/local/bin/seqtk
[07:15:13] Found parallel - /usr/local/bin/parallel
[07:15:13] Found freebayes - /usr/local/bin/freebayes
[07:15:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:15:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:15:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:15:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:15:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:15:13] Found gzip - /bin/gzip
[07:15:13] Found vt - /usr/local/bin/vt
[07:15:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:15:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:15:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:15:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:15:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:15:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:15:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:15:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:15:24] This is snippy 4.6.0Show full stderr[07:15:24] This is snippy 4.6.0
[07:15:24] Written by Torsten Seemann
[07:15:24] Obtained from https://github.com/tseemann/snippy
[07:15:24] Detected operating system: linux
[07:15:24] Enabling bundled linux tools.
[07:15:24] Found bwa - /usr/local/bin/bwa
[07:15:24] Found bcftools - /usr/local/bin/bcftools
[07:15:24] Found samtools - /usr/local/bin/samtools
[07:15:24] Found java - /usr/local/bin/java
[07:15:24] Found snpEff - /usr/local/bin/snpEff
[07:15:24] Found samclip - /usr/local/bin/samclip
[07:15:24] Found seqtk - /usr/local/bin/seqtk
[07:15:24] Found parallel - /usr/local/bin/parallel
[07:15:24] Found freebayes - /usr/local/bin/freebayes
[07:15:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:15:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:15:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:15:24] Found vcfuniq - /usr/local/bin/vcfuniq
[07:15:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:15:24] Found gzip - /bin/gzip
[07:15:24] Found vt - /usr/local/bin/vt
[07:15:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:15:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:15:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:15:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:15:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:15:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:15:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:15:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:16:07] This is snippy 4.6.0Show full stderr[07:16:07] This is snippy 4.6.0
[07:16:07] Written by Torsten Seemann
[07:16:07] Obtained from https://github.com/tseemann/snippy
[07:16:07] Detected operating system: linux
[07:16:07] Enabling bundled linux tools.
[07:16:07] Found bwa - /usr/local/bin/bwa
[07:16:07] Found bcftools - /usr/local/bin/bcftools
[07:16:07] Found samtools - /usr/local/bin/samtools
[07:16:07] Found java - /usr/local/bin/java
[07:16:07] Found snpEff - /usr/local/bin/snpEff
[07:16:07] Found samclip - /usr/local/bin/samclip
[07:16:07] Found seqtk - /usr/local/bin/seqtk
[07:16:07] Found parallel - /usr/local/bin/parallel
[07:16:07] Found freebayes - /usr/local/bin/freebayes
[07:16:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:16:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:16:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:16:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:16:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:16:07] Found gzip - /bin/gzip
[07:16:07] Found vt - /usr/local/bin/vt
[07:16:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:16:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:16:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:16:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:16:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:16:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:16:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:16:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:16:19] This is snippy 4.6.0Show full stderr[07:16:19] This is snippy 4.6.0
[07:16:19] Written by Torsten Seemann
[07:16:19] Obtained from https://github.com/tseemann/snippy
[07:16:19] Detected operating system: linux
[07:16:19] Enabling bundled linux tools.
[07:16:19] Found bwa - /usr/local/bin/bwa
[07:16:19] Found bcftools - /usr/local/bin/bcftools
[07:16:19] Found samtools - /usr/local/bin/samtools
[07:16:19] Found java - /usr/local/bin/java
[07:16:19] Found snpEff - /usr/local/bin/snpEff
[07:16:19] Found samclip - /usr/local/bin/samclip
[07:16:19] Found seqtk - /usr/local/bin/seqtk
[07:16:19] Found parallel - /usr/local/bin/parallel
[07:16:19] Found freebayes - /usr/local/bin/freebayes
[07:16:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:16:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:16:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:16:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:16:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:16:19] Found gzip - /bin/gzip
[07:16:19] Found vt - /usr/local/bin/vt
[07:16:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:16:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:16:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:16:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:16:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:16:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:16:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:16:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:29:19] This is snippy 4.6.0Show full stderr[07:29:19] This is snippy 4.6.0
[07:29:19] Written by Torsten Seemann
[07:29:19] Obtained from https://github.com/tseemann/snippy
[07:29:19] Detected operating system: linux
[07:29:19] Enabling bundled linux tools.
[07:29:19] Found bwa - /usr/local/bin/bwa
[07:29:19] Found bcftools - /usr/local/bin/bcftools
[07:29:19] Found samtools - /usr/local/bin/samtools
[07:29:19] Found java - /usr/local/bin/java
[07:29:19] Found snpEff - /usr/local/bin/snpEff
[07:29:19] Found samclip - /usr/local/bin/samclip
[07:29:19] Found seqtk - /usr/local/bin/seqtk
[07:29:19] Found parallel - /usr/local/bin/parallel
[07:29:19] Found freebayes - /usr/local/bin/freebayes
[07:29:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:29:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:29:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:29:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:29:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:29:19] Found gzip - /bin/gzip
[07:29:19] Found vt - /usr/local/bin/vt
[07:29:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:29:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:29:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:29:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:29:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:29:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:29:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:29:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:31:57] This is snippy 4.6.0Show full stderr[07:31:57] This is snippy 4.6.0
[07:31:57] Written by Torsten Seemann
[07:31:57] Obtained from https://github.com/tseemann/snippy
[07:31:57] Detected operating system: linux
[07:31:57] Enabling bundled linux tools.
[07:31:57] Found bwa - /usr/local/bin/bwa
[07:31:57] Found bcftools - /usr/local/bin/bcftools
[07:31:57] Found samtools - /usr/local/bin/samtools
[07:31:57] Found java - /usr/local/bin/java
[07:31:57] Found snpEff - /usr/local/bin/snpEff
[07:31:57] Found samclip - /usr/local/bin/samclip
[07:31:57] Found seqtk - /usr/local/bin/seqtk
[07:31:57] Found parallel - /usr/local/bin/parallel
[07:31:57] Found freebayes - /usr/local/bin/freebayes
[07:31:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:31:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:31:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:31:57] Found vcfuniq - /usr/local/bin/vcfuniq
[07:31:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:31:57] Found gzip - /bin/gzip
[07:31:57] Found vt - /usr/local/bin/vt
[07:31:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:31:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:31:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:31:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:31:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:31:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:31:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:31:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:29:04] This is snippy 4.6.0Show full stderr[07:29:04] This is snippy 4.6.0
[07:29:04] Written by Torsten Seemann
[07:29:04] Obtained from https://github.com/tseemann/snippy
[07:29:04] Detected operating system: linux
[07:29:04] Enabling bundled linux tools.
[07:29:04] Found bwa - /usr/local/bin/bwa
[07:29:04] Found bcftools - /usr/local/bin/bcftools
[07:29:04] Found samtools - /usr/local/bin/samtools
[07:29:04] Found java - /usr/local/bin/java
[07:29:04] Found snpEff - /usr/local/bin/snpEff
[07:29:04] Found samclip - /usr/local/bin/samclip
[07:29:04] Found seqtk - /usr/local/bin/seqtk
[07:29:04] Found parallel - /usr/local/bin/parallel
[07:29:04] Found freebayes - /usr/local/bin/freebayes
[07:29:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:29:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:29:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:29:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:29:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:29:04] Found gzip - /bin/gzip
[07:29:04] Found vt - /usr/local/bin/vt
[07:29:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:29:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:29:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:29:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:29:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:29:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:29:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:29:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:29:49] This is snippy 4.6.0Show full stderr[07:29:49] This is snippy 4.6.0
[07:29:49] Written by Torsten Seemann
[07:29:49] Obtained from https://github.com/tseemann/snippy
[07:29:49] Detected operating system: linux
[07:29:49] Enabling bundled linux tools.
[07:29:49] Found bwa - /usr/local/bin/bwa
[07:29:49] Found bcftools - /usr/local/bin/bcftools
[07:29:49] Found samtools - /usr/local/bin/samtools
[07:29:49] Found java - /usr/local/bin/java
[07:29:49] Found snpEff - /usr/local/bin/snpEff
[07:29:49] Found samclip - /usr/local/bin/samclip
[07:29:49] Found seqtk - /usr/local/bin/seqtk
[07:29:49] Found parallel - /usr/local/bin/parallel
[07:29:49] Found freebayes - /usr/local/bin/freebayes
[07:29:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:29:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:29:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:29:49] Found vcfuniq - /usr/local/bin/vcfuniq
[07:29:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:29:49] Found gzip - /bin/gzip
[07:29:49] Found vt - /usr/local/bin/vt
[07:29:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:29:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:29:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:29:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:29:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:29:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:29:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:29:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:28:12] This is snippy 4.6.0Show full stderr[07:28:12] This is snippy 4.6.0
[07:28:12] Written by Torsten Seemann
[07:28:12] Obtained from https://github.com/tseemann/snippy
[07:28:12] Detected operating system: linux
[07:28:12] Enabling bundled linux tools.
[07:28:12] Found bwa - /usr/local/bin/bwa
[07:28:12] Found bcftools - /usr/local/bin/bcftools
[07:28:12] Found samtools - /usr/local/bin/samtools
[07:28:12] Found java - /usr/local/bin/java
[07:28:12] Found snpEff - /usr/local/bin/snpEff
[07:28:12] Found samclip - /usr/local/bin/samclip
[07:28:12] Found seqtk - /usr/local/bin/seqtk
[07:28:12] Found parallel - /usr/local/bin/parallel
[07:28:12] Found freebayes - /usr/local/bin/freebayes
[07:28:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:28:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:28:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:28:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:28:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:28:13] Found gzip - /bin/gzip
[07:28:13] Found vt - /usr/local/bin/vt
[07:28:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:28:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:28:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:28:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:28:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:28:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:28:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:28:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:28:15] This is snippy 4.6.0Show full stderr[07:28:15] This is snippy 4.6.0
[07:28:15] Written by Torsten Seemann
[07:28:15] Obtained from https://github.com/tseemann/snippy
[07:28:15] Detected operating system: linux
[07:28:15] Enabling bundled linux tools.
[07:28:16] Found bwa - /usr/local/bin/bwa
[07:28:16] Found bcftools - /usr/local/bin/bcftools
[07:28:16] Found samtools - /usr/local/bin/samtools
[07:28:16] Found java - /usr/local/bin/java
[07:28:16] Found snpEff - /usr/local/bin/snpEff
[07:28:16] Found samclip - /usr/local/bin/samclip
[07:28:16] Found seqtk - /usr/local/bin/seqtk
[07:28:16] Found parallel - /usr/local/bin/parallel
[07:28:16] Found freebayes - /usr/local/bin/freebayes
[07:28:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:28:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:28:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:28:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:28:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:28:16] Found gzip - /bin/gzip
[07:28:16] Found vt - /usr/local/bin/vt
[07:28:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:28:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:28:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:28:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:28:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:28:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:28:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:28:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:28:25] This is snippy 4.6.0Show full stderr[07:28:25] This is snippy 4.6.0
[07:28:25] Written by Torsten Seemann
[07:28:25] Obtained from https://github.com/tseemann/snippy
[07:28:25] Detected operating system: linux
[07:28:25] Enabling bundled linux tools.
[07:28:25] Found bwa - /usr/local/bin/bwa
[07:28:25] Found bcftools - /usr/local/bin/bcftools
[07:28:25] Found samtools - /usr/local/bin/samtools
[07:28:25] Found java - /usr/local/bin/java
[07:28:25] Found snpEff - /usr/local/bin/snpEff
[07:28:26] Found samclip - /usr/local/bin/samclip
[07:28:26] Found seqtk - /usr/local/bin/seqtk
[07:28:26] Found parallel - /usr/local/bin/parallel
[07:28:26] Found freebayes - /usr/local/bin/freebayes
[07:28:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:28:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:28:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:28:26] Found vcfuniq - /usr/local/bin/vcfuniq
[07:28:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:28:26] Found gzip - /bin/gzip
[07:28:26] Found vt - /usr/local/bin/vt
[07:28:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:28:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:28:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:28:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:28:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:28:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:28:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:28:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:28:28] This is snippy 4.6.0Show full stderr[07:28:28] This is snippy 4.6.0
[07:28:28] Written by Torsten Seemann
[07:28:28] Obtained from https://github.com/tseemann/snippy
[07:28:28] Detected operating system: linux
[07:28:28] Enabling bundled linux tools.
[07:28:28] Found bwa - /usr/local/bin/bwa
[07:28:28] Found bcftools - /usr/local/bin/bcftools
[07:28:28] Found samtools - /usr/local/bin/samtools
[07:28:28] Found java - /usr/local/bin/java
[07:28:29] Found snpEff - /usr/local/bin/snpEff
[07:28:29] Found samclip - /usr/local/bin/samclip
[07:28:29] Found seqtk - /usr/local/bin/seqtk
[07:28:29] Found parallel - /usr/local/bin/parallel
[07:28:29] Found freebayes - /usr/local/bin/freebayes
[07:28:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:28:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:28:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:28:29] Found vcfuniq - /usr/local/bin/vcfuniq
[07:28:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:28:29] Found gzip - /bin/gzip
[07:28:29] Found vt - /usr/local/bin/vt
[07:28:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:28:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:28:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:28:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:28:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:28:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:28:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:28:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:29:22] This is snippy 4.6.0Show full stderr[07:29:22] This is snippy 4.6.0
[07:29:22] Written by Torsten Seemann
[07:29:22] Obtained from https://github.com/tseemann/snippy
[07:29:22] Detected operating system: linux
[07:29:22] Enabling bundled linux tools.
[07:29:22] Found bwa - /usr/local/bin/bwa
[07:29:22] Found bcftools - /usr/local/bin/bcftools
[07:29:22] Found samtools - /usr/local/bin/samtools
[07:29:22] Found java - /usr/local/bin/java
[07:29:22] Found snpEff - /usr/local/bin/snpEff
[07:29:22] Found samclip - /usr/local/bin/samclip
[07:29:22] Found seqtk - /usr/local/bin/seqtk
[07:29:22] Found parallel - /usr/local/bin/parallel
[07:29:22] Found freebayes - /usr/local/bin/freebayes
[07:29:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:29:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:29:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:29:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:29:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:29:22] Found gzip - /bin/gzip
[07:29:22] Found vt - /usr/local/bin/vt
[07:29:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:29:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:29:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:29:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:29:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:29:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:29:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:29:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:29:40] This is snippy 4.6.0Show full stderr[07:29:40] This is snippy 4.6.0
[07:29:40] Written by Torsten Seemann
[07:29:40] Obtained from https://github.com/tseemann/snippy
[07:29:40] Detected operating system: linux
[07:29:40] Enabling bundled linux tools.
[07:29:40] Found bwa - /usr/local/bin/bwa
[07:29:40] Found bcftools - /usr/local/bin/bcftools
[07:29:40] Found samtools - /usr/local/bin/samtools
[07:29:40] Found java - /usr/local/bin/java
[07:29:40] Found snpEff - /usr/local/bin/snpEff
[07:29:40] Found samclip - /usr/local/bin/samclip
[07:29:40] Found seqtk - /usr/local/bin/seqtk
[07:29:40] Found parallel - /usr/local/bin/parallel
[07:29:40] Found freebayes - /usr/local/bin/freebayes
[07:29:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:29:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:29:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:29:40] Found vcfuniq - /usr/local/bin/vcfuniq
[07:29:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:29:40] Found gzip - /bin/gzip
[07:29:40] Found vt - /usr/local/bin/vt
[07:29:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:29:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:29:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:29:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:29:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:29:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:29:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:29:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:29:07] This is snippy 4.6.0Show full stderr[07:29:07] This is snippy 4.6.0
[07:29:07] Written by Torsten Seemann
[07:29:07] Obtained from https://github.com/tseemann/snippy
[07:29:07] Detected operating system: linux
[07:29:07] Enabling bundled linux tools.
[07:29:07] Found bwa - /usr/local/bin/bwa
[07:29:07] Found bcftools - /usr/local/bin/bcftools
[07:29:07] Found samtools - /usr/local/bin/samtools
[07:29:07] Found java - /usr/local/bin/java
[07:29:07] Found snpEff - /usr/local/bin/snpEff
[07:29:07] Found samclip - /usr/local/bin/samclip
[07:29:07] Found seqtk - /usr/local/bin/seqtk
[07:29:07] Found parallel - /usr/local/bin/parallel
[07:29:07] Found freebayes - /usr/local/bin/freebayes
[07:29:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:29:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:29:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:29:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:29:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:29:07] Found gzip - /bin/gzip
[07:29:07] Found vt - /usr/local/bin/vt
[07:29:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:29:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:29:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:29:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:29:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:29:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:29:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:29:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:30:22] This is snippy 4.6.0Show full stderr[07:30:22] This is snippy 4.6.0
[07:30:22] Written by Torsten Seemann
[07:30:22] Obtained from https://github.com/tseemann/snippy
[07:30:22] Detected operating system: linux
[07:30:22] Enabling bundled linux tools.
[07:30:22] Found bwa - /usr/local/bin/bwa
[07:30:22] Found bcftools - /usr/local/bin/bcftools
[07:30:22] Found samtools - /usr/local/bin/samtools
[07:30:22] Found java - /usr/local/bin/java
[07:30:22] Found snpEff - /usr/local/bin/snpEff
[07:30:22] Found samclip - /usr/local/bin/samclip
[07:30:22] Found seqtk - /usr/local/bin/seqtk
[07:30:22] Found parallel - /usr/local/bin/parallel
[07:30:22] Found freebayes - /usr/local/bin/freebayes
[07:30:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:30:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:30:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:30:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:30:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:30:22] Found gzip - /bin/gzip
[07:30:22] Found vt - /usr/local/bin/vt
[07:30:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:30:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:30:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:30:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:30:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:30:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:30:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:30:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:30:54] This is snippy 4.6.0Show full stderr[07:30:54] This is snippy 4.6.0
[07:30:54] Written by Torsten Seemann
[07:30:54] Obtained from https://github.com/tseemann/snippy
[07:30:54] Detected operating system: linux
[07:30:54] Enabling bundled linux tools.
[07:30:54] Found bwa - /usr/local/bin/bwa
[07:30:54] Found bcftools - /usr/local/bin/bcftools
[07:30:54] Found samtools - /usr/local/bin/samtools
[07:30:54] Found java - /usr/local/bin/java
[07:30:54] Found snpEff - /usr/local/bin/snpEff
[07:30:54] Found samclip - /usr/local/bin/samclip
[07:30:54] Found seqtk - /usr/local/bin/seqtk
[07:30:54] Found parallel - /usr/local/bin/parallel
[07:30:54] Found freebayes - /usr/local/bin/freebayes
[07:30:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:30:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:30:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:30:54] Found vcfuniq - /usr/local/bin/vcfuniq
[07:30:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:30:54] Found gzip - /bin/gzip
[07:30:54] Found vt - /usr/local/bin/vt
[07:30:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:30:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:30:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:30:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:30:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:30:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:30:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:30:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:31:28] This is snippy 4.6.0Show full stderr[07:31:28] This is snippy 4.6.0
[07:31:28] Written by Torsten Seemann
[07:31:28] Obtained from https://github.com/tseemann/snippy
[07:31:28] Detected operating system: linux
[07:31:28] Enabling bundled linux tools.
[07:31:28] Found bwa - /usr/local/bin/bwa
[07:31:28] Found bcftools - /usr/local/bin/bcftools
[07:31:28] Found samtools - /usr/local/bin/samtools
[07:31:28] Found java - /usr/local/bin/java
[07:31:28] Found snpEff - /usr/local/bin/snpEff
[07:31:28] Found samclip - /usr/local/bin/samclip
[07:31:28] Found seqtk - /usr/local/bin/seqtk
[07:31:28] Found parallel - /usr/local/bin/parallel
[07:31:28] Found freebayes - /usr/local/bin/freebayes
[07:31:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:31:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:31:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:31:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:31:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:31:28] Found gzip - /bin/gzip
[07:31:28] Found vt - /usr/local/bin/vt
[07:31:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:31:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:31:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:31:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:31:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:31:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:31:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:31:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:32:24] This is snippy 4.6.0Show full stderr[07:32:24] This is snippy 4.6.0
[07:32:24] Written by Torsten Seemann
[07:32:24] Obtained from https://github.com/tseemann/snippy
[07:32:24] Detected operating system: linux
[07:32:24] Enabling bundled linux tools.
[07:32:24] Found bwa - /usr/local/bin/bwa
[07:32:24] Found bcftools - /usr/local/bin/bcftools
[07:32:24] Found samtools - /usr/local/bin/samtools
[07:32:24] Found java - /usr/local/bin/java
[07:32:24] Found snpEff - /usr/local/bin/snpEff
[07:32:24] Found samclip - /usr/local/bin/samclip
[07:32:24] Found seqtk - /usr/local/bin/seqtk
[07:32:24] Found parallel - /usr/local/bin/parallel
[07:32:24] Found freebayes - /usr/local/bin/freebayes
[07:32:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:24] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:24] Found gzip - /bin/gzip
[07:32:24] Found vt - /usr/local/bin/vt
[07:32:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:35:48] This is snippy 4.6.0Show full stderr[07:35:48] This is snippy 4.6.0
[07:35:48] Written by Torsten Seemann
[07:35:48] Obtained from https://github.com/tseemann/snippy
[07:35:48] Detected operating system: linux
[07:35:48] Enabling bundled linux tools.
[07:35:48] Found bwa - /usr/local/bin/bwa
[07:35:48] Found bcftools - /usr/local/bin/bcftools
[07:35:48] Found samtools - /usr/local/bin/samtools
[07:35:48] Found java - /usr/local/bin/java
[07:35:48] Found snpEff - /usr/local/bin/snpEff
[07:35:48] Found samclip - /usr/local/bin/samclip
[07:35:48] Found seqtk - /usr/local/bin/seqtk
[07:35:48] Found parallel - /usr/local/bin/parallel
[07:35:48] Found freebayes - /usr/local/bin/freebayes
[07:35:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:35:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:35:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:35:48] Found vcfuniq - /usr/local/bin/vcfuniq
[07:35:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:35:48] Found gzip - /bin/gzip
[07:35:48] Found vt - /usr/local/bin/vt
[07:35:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:35:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:35:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:35:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:35:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:35:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:35:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:35:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:35:51] This is snippy 4.6.0Show full stderr[07:35:51] This is snippy 4.6.0
[07:35:51] Written by Torsten Seemann
[07:35:51] Obtained from https://github.com/tseemann/snippy
[07:35:51] Detected operating system: linux
[07:35:51] Enabling bundled linux tools.
[07:35:51] Found bwa - /usr/local/bin/bwa
[07:35:51] Found bcftools - /usr/local/bin/bcftools
[07:35:51] Found samtools - /usr/local/bin/samtools
[07:35:51] Found java - /usr/local/bin/java
[07:35:51] Found snpEff - /usr/local/bin/snpEff
[07:35:51] Found samclip - /usr/local/bin/samclip
[07:35:51] Found seqtk - /usr/local/bin/seqtk
[07:35:51] Found parallel - /usr/local/bin/parallel
[07:35:51] Found freebayes - /usr/local/bin/freebayes
[07:35:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:35:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:35:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:35:51] Found vcfuniq - /usr/local/bin/vcfuniq
[07:35:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:35:51] Found gzip - /bin/gzip
[07:35:51] Found vt - /usr/local/bin/vt
[07:35:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:35:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:35:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:35:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:35:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:35:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:35:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:35:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:35:54] This is snippy 4.6.0Show full stderr[07:35:54] This is snippy 4.6.0
[07:35:54] Written by Torsten Seemann
[07:35:54] Obtained from https://github.com/tseemann/snippy
[07:35:54] Detected operating system: linux
[07:35:54] Enabling bundled linux tools.
[07:35:54] Found bwa - /usr/local/bin/bwa
[07:35:54] Found bcftools - /usr/local/bin/bcftools
[07:35:54] Found samtools - /usr/local/bin/samtools
[07:35:54] Found java - /usr/local/bin/java
[07:35:54] Found snpEff - /usr/local/bin/snpEff
[07:35:54] Found samclip - /usr/local/bin/samclip
[07:35:54] Found seqtk - /usr/local/bin/seqtk
[07:35:54] Found parallel - /usr/local/bin/parallel
[07:35:54] Found freebayes - /usr/local/bin/freebayes
[07:35:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:35:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:35:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:35:54] Found vcfuniq - /usr/local/bin/vcfuniq
[07:35:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:35:54] Found gzip - /bin/gzip
[07:35:54] Found vt - /usr/local/bin/vt
[07:35:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:35:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:35:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:35:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:35:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:35:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:35:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:35:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:04] This is snippy 4.6.0Show full stderr[07:36:04] This is snippy 4.6.0
[07:36:04] Written by Torsten Seemann
[07:36:04] Obtained from https://github.com/tseemann/snippy
[07:36:04] Detected operating system: linux
[07:36:04] Enabling bundled linux tools.
[07:36:04] Found bwa - /usr/local/bin/bwa
[07:36:04] Found bcftools - /usr/local/bin/bcftools
[07:36:04] Found samtools - /usr/local/bin/samtools
[07:36:04] Found java - /usr/local/bin/java
[07:36:04] Found snpEff - /usr/local/bin/snpEff
[07:36:04] Found samclip - /usr/local/bin/samclip
[07:36:04] Found seqtk - /usr/local/bin/seqtk
[07:36:04] Found parallel - /usr/local/bin/parallel
[07:36:04] Found freebayes - /usr/local/bin/freebayes
[07:36:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:04] Found gzip - /bin/gzip
[07:36:04] Found vt - /usr/local/bin/vt
[07:36:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:29:55] This is snippy 4.6.0Show full stderr[07:29:55] This is snippy 4.6.0
[07:29:55] Written by Torsten Seemann
[07:29:55] Obtained from https://github.com/tseemann/snippy
[07:29:55] Detected operating system: linux
[07:29:55] Enabling bundled linux tools.
[07:29:55] Found bwa - /usr/local/bin/bwa
[07:29:55] Found bcftools - /usr/local/bin/bcftools
[07:29:55] Found samtools - /usr/local/bin/samtools
[07:29:55] Found java - /usr/local/bin/java
[07:29:55] Found snpEff - /usr/local/bin/snpEff
[07:29:55] Found samclip - /usr/local/bin/samclip
[07:29:55] Found seqtk - /usr/local/bin/seqtk
[07:29:55] Found parallel - /usr/local/bin/parallel
[07:29:55] Found freebayes - /usr/local/bin/freebayes
[07:29:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:29:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:29:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:29:55] Found vcfuniq - /usr/local/bin/vcfuniq
[07:29:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:29:55] Found gzip - /bin/gzip
[07:29:55] Found vt - /usr/local/bin/vt
[07:29:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:29:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:29:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:29:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:29:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:29:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:29:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:29:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:30:07] This is snippy 4.6.0Show full stderr[07:30:07] This is snippy 4.6.0
[07:30:07] Written by Torsten Seemann
[07:30:07] Obtained from https://github.com/tseemann/snippy
[07:30:07] Detected operating system: linux
[07:30:07] Enabling bundled linux tools.
[07:30:07] Found bwa - /usr/local/bin/bwa
[07:30:07] Found bcftools - /usr/local/bin/bcftools
[07:30:07] Found samtools - /usr/local/bin/samtools
[07:30:07] Found java - /usr/local/bin/java
[07:30:07] Found snpEff - /usr/local/bin/snpEff
[07:30:07] Found samclip - /usr/local/bin/samclip
[07:30:07] Found seqtk - /usr/local/bin/seqtk
[07:30:07] Found parallel - /usr/local/bin/parallel
[07:30:07] Found freebayes - /usr/local/bin/freebayes
[07:30:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:30:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:30:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:30:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:30:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:30:07] Found gzip - /bin/gzip
[07:30:07] Found vt - /usr/local/bin/vt
[07:30:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:30:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:30:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:30:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:30:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:30:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:30:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:30:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:30:13] This is snippy 4.6.0Show full stderr[07:30:13] This is snippy 4.6.0
[07:30:13] Written by Torsten Seemann
[07:30:13] Obtained from https://github.com/tseemann/snippy
[07:30:13] Detected operating system: linux
[07:30:13] Enabling bundled linux tools.
[07:30:13] Found bwa - /usr/local/bin/bwa
[07:30:13] Found bcftools - /usr/local/bin/bcftools
[07:30:13] Found samtools - /usr/local/bin/samtools
[07:30:13] Found java - /usr/local/bin/java
[07:30:13] Found snpEff - /usr/local/bin/snpEff
[07:30:13] Found samclip - /usr/local/bin/samclip
[07:30:13] Found seqtk - /usr/local/bin/seqtk
[07:30:13] Found parallel - /usr/local/bin/parallel
[07:30:13] Found freebayes - /usr/local/bin/freebayes
[07:30:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:30:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:30:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:30:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:30:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:30:13] Found gzip - /bin/gzip
[07:30:13] Found vt - /usr/local/bin/vt
[07:30:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:30:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:30:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:30:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:30:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:30:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:30:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:30:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:30:43] This is snippy 4.6.0Show full stderr[07:30:43] This is snippy 4.6.0
[07:30:43] Written by Torsten Seemann
[07:30:43] Obtained from https://github.com/tseemann/snippy
[07:30:43] Detected operating system: linux
[07:30:43] Enabling bundled linux tools.
[07:30:43] Found bwa - /usr/local/bin/bwa
[07:30:43] Found bcftools - /usr/local/bin/bcftools
[07:30:43] Found samtools - /usr/local/bin/samtools
[07:30:43] Found java - /usr/local/bin/java
[07:30:43] Found snpEff - /usr/local/bin/snpEff
[07:30:43] Found samclip - /usr/local/bin/samclip
[07:30:43] Found seqtk - /usr/local/bin/seqtk
[07:30:43] Found parallel - /usr/local/bin/parallel
[07:30:43] Found freebayes - /usr/local/bin/freebayes
[07:30:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:30:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:30:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:30:43] Found vcfuniq - /usr/local/bin/vcfuniq
[07:30:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:30:43] Found gzip - /bin/gzip
[07:30:43] Found vt - /usr/local/bin/vt
[07:30:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:30:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:30:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:30:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:30:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:30:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:30:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:30:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:30:46] This is snippy 4.6.0Show full stderr[07:30:46] This is snippy 4.6.0
[07:30:46] Written by Torsten Seemann
[07:30:46] Obtained from https://github.com/tseemann/snippy
[07:30:46] Detected operating system: linux
[07:30:46] Enabling bundled linux tools.
[07:30:46] Found bwa - /usr/local/bin/bwa
[07:30:46] Found bcftools - /usr/local/bin/bcftools
[07:30:46] Found samtools - /usr/local/bin/samtools
[07:30:46] Found java - /usr/local/bin/java
[07:30:46] Found snpEff - /usr/local/bin/snpEff
[07:30:46] Found samclip - /usr/local/bin/samclip
[07:30:46] Found seqtk - /usr/local/bin/seqtk
[07:30:46] Found parallel - /usr/local/bin/parallel
[07:30:46] Found freebayes - /usr/local/bin/freebayes
[07:30:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:30:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:30:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:30:46] Found vcfuniq - /usr/local/bin/vcfuniq
[07:30:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:30:46] Found gzip - /bin/gzip
[07:30:46] Found vt - /usr/local/bin/vt
[07:30:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:30:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:30:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:30:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:30:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:30:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:30:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:30:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:31:00] This is snippy 4.6.0Show full stderr[07:31:00] This is snippy 4.6.0
[07:31:00] Written by Torsten Seemann
[07:31:00] Obtained from https://github.com/tseemann/snippy
[07:31:00] Detected operating system: linux
[07:31:00] Enabling bundled linux tools.
[07:31:00] Found bwa - /usr/local/bin/bwa
[07:31:00] Found bcftools - /usr/local/bin/bcftools
[07:31:00] Found samtools - /usr/local/bin/samtools
[07:31:00] Found java - /usr/local/bin/java
[07:31:00] Found snpEff - /usr/local/bin/snpEff
[07:31:00] Found samclip - /usr/local/bin/samclip
[07:31:00] Found seqtk - /usr/local/bin/seqtk
[07:31:00] Found parallel - /usr/local/bin/parallel
[07:31:00] Found freebayes - /usr/local/bin/freebayes
[07:31:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:31:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:31:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:31:00] Found vcfuniq - /usr/local/bin/vcfuniq
[07:31:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:31:00] Found gzip - /bin/gzip
[07:31:00] Found vt - /usr/local/bin/vt
[07:31:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:31:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:31:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:31:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:31:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:31:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:31:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:31:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:33:47] This is snippy 4.6.0Show full stderr[07:33:47] This is snippy 4.6.0
[07:33:47] Written by Torsten Seemann
[07:33:47] Obtained from https://github.com/tseemann/snippy
[07:33:47] Detected operating system: linux
[07:33:47] Enabling bundled linux tools.
[07:33:47] Found bwa - /usr/local/bin/bwa
[07:33:47] Found bcftools - /usr/local/bin/bcftools
[07:33:47] Found samtools - /usr/local/bin/samtools
[07:33:47] Found java - /usr/local/bin/java
[07:33:47] Found snpEff - /usr/local/bin/snpEff
[07:33:47] Found samclip - /usr/local/bin/samclip
[07:33:47] Found seqtk - /usr/local/bin/seqtk
[07:33:47] Found parallel - /usr/local/bin/parallel
[07:33:47] Found freebayes - /usr/local/bin/freebayes
[07:33:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:33:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:33:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:33:47] Found vcfuniq - /usr/local/bin/vcfuniq
[07:33:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:33:47] Found gzip - /bin/gzip
[07:33:47] Found vt - /usr/local/bin/vt
[07:33:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:33:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:33:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:33:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:33:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:33:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:33:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:33:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:34:40] This is snippy 4.6.0Show full stderr[07:34:40] This is snippy 4.6.0
[07:34:40] Written by Torsten Seemann
[07:34:40] Obtained from https://github.com/tseemann/snippy
[07:34:40] Detected operating system: linux
[07:34:40] Enabling bundled linux tools.
[07:34:40] Found bwa - /usr/local/bin/bwa
[07:34:40] Found bcftools - /usr/local/bin/bcftools
[07:34:40] Found samtools - /usr/local/bin/samtools
[07:34:40] Found java - /usr/local/bin/java
[07:34:40] Found snpEff - /usr/local/bin/snpEff
[07:34:40] Found samclip - /usr/local/bin/samclip
[07:34:40] Found seqtk - /usr/local/bin/seqtk
[07:34:40] Found parallel - /usr/local/bin/parallel
[07:34:40] Found freebayes - /usr/local/bin/freebayes
[07:34:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:34:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:34:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:34:40] Found vcfuniq - /usr/local/bin/vcfuniq
[07:34:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:34:40] Found gzip - /bin/gzip
[07:34:40] Found vt - /usr/local/bin/vt
[07:34:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:34:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:34:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:34:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:34:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:34:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:34:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:34:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:34:43] This is snippy 4.6.0Show full stderr[07:34:43] This is snippy 4.6.0
[07:34:43] Written by Torsten Seemann
[07:34:43] Obtained from https://github.com/tseemann/snippy
[07:34:43] Detected operating system: linux
[07:34:43] Enabling bundled linux tools.
[07:34:43] Found bwa - /usr/local/bin/bwa
[07:34:43] Found bcftools - /usr/local/bin/bcftools
[07:34:43] Found samtools - /usr/local/bin/samtools
[07:34:43] Found java - /usr/local/bin/java
[07:34:43] Found snpEff - /usr/local/bin/snpEff
[07:34:43] Found samclip - /usr/local/bin/samclip
[07:34:43] Found seqtk - /usr/local/bin/seqtk
[07:34:43] Found parallel - /usr/local/bin/parallel
[07:34:43] Found freebayes - /usr/local/bin/freebayes
[07:34:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:34:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:34:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:34:43] Found vcfuniq - /usr/local/bin/vcfuniq
[07:34:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:34:43] Found gzip - /bin/gzip
[07:34:43] Found vt - /usr/local/bin/vt
[07:34:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:34:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:34:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:34:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:34:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:34:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:34:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:34:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:35:07] This is snippy 4.6.0Show full stderr[07:35:07] This is snippy 4.6.0
[07:35:07] Written by Torsten Seemann
[07:35:07] Obtained from https://github.com/tseemann/snippy
[07:35:07] Detected operating system: linux
[07:35:07] Enabling bundled linux tools.
[07:35:07] Found bwa - /usr/local/bin/bwa
[07:35:07] Found bcftools - /usr/local/bin/bcftools
[07:35:07] Found samtools - /usr/local/bin/samtools
[07:35:07] Found java - /usr/local/bin/java
[07:35:07] Found snpEff - /usr/local/bin/snpEff
[07:35:07] Found samclip - /usr/local/bin/samclip
[07:35:07] Found seqtk - /usr/local/bin/seqtk
[07:35:07] Found parallel - /usr/local/bin/parallel
[07:35:07] Found freebayes - /usr/local/bin/freebayes
[07:35:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:35:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:35:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:35:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:35:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:35:07] Found gzip - /bin/gzip
[07:35:07] Found vt - /usr/local/bin/vt
[07:35:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:35:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:35:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:35:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:35:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:35:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:35:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:35:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:35:24] This is snippy 4.6.0Show full stderr[07:35:24] This is snippy 4.6.0
[07:35:24] Written by Torsten Seemann
[07:35:24] Obtained from https://github.com/tseemann/snippy
[07:35:24] Detected operating system: linux
[07:35:24] Enabling bundled linux tools.
[07:35:24] Found bwa - /usr/local/bin/bwa
[07:35:24] Found bcftools - /usr/local/bin/bcftools
[07:35:24] Found samtools - /usr/local/bin/samtools
[07:35:24] Found java - /usr/local/bin/java
[07:35:24] Found snpEff - /usr/local/bin/snpEff
[07:35:24] Found samclip - /usr/local/bin/samclip
[07:35:24] Found seqtk - /usr/local/bin/seqtk
[07:35:24] Found parallel - /usr/local/bin/parallel
[07:35:24] Found freebayes - /usr/local/bin/freebayes
[07:35:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:35:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:35:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:35:24] Found vcfuniq - /usr/local/bin/vcfuniq
[07:35:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:35:24] Found gzip - /bin/gzip
[07:35:24] Found vt - /usr/local/bin/vt
[07:35:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:35:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:35:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:35:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:35:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:35:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:35:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:35:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:32:42] This is snippy 4.6.0Show full stderr[07:32:42] This is snippy 4.6.0
[07:32:42] Written by Torsten Seemann
[07:32:42] Obtained from https://github.com/tseemann/snippy
[07:32:42] Detected operating system: linux
[07:32:42] Enabling bundled linux tools.
[07:32:42] Found bwa - /usr/local/bin/bwa
[07:32:42] Found bcftools - /usr/local/bin/bcftools
[07:32:42] Found samtools - /usr/local/bin/samtools
[07:32:42] Found java - /usr/local/bin/java
[07:32:42] Found snpEff - /usr/local/bin/snpEff
[07:32:42] Found samclip - /usr/local/bin/samclip
[07:32:42] Found seqtk - /usr/local/bin/seqtk
[07:32:42] Found parallel - /usr/local/bin/parallel
[07:32:42] Found freebayes - /usr/local/bin/freebayes
[07:32:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:42] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:42] Found gzip - /bin/gzip
[07:32:42] Found vt - /usr/local/bin/vt
[07:32:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:33:29] This is snippy 4.6.0Show full stderr[07:33:29] This is snippy 4.6.0
[07:33:29] Written by Torsten Seemann
[07:33:29] Obtained from https://github.com/tseemann/snippy
[07:33:29] Detected operating system: linux
[07:33:29] Enabling bundled linux tools.
[07:33:29] Found bwa - /usr/local/bin/bwa
[07:33:29] Found bcftools - /usr/local/bin/bcftools
[07:33:29] Found samtools - /usr/local/bin/samtools
[07:33:29] Found java - /usr/local/bin/java
[07:33:29] Found snpEff - /usr/local/bin/snpEff
[07:33:29] Found samclip - /usr/local/bin/samclip
[07:33:29] Found seqtk - /usr/local/bin/seqtk
[07:33:29] Found parallel - /usr/local/bin/parallel
[07:33:29] Found freebayes - /usr/local/bin/freebayes
[07:33:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:33:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:33:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:33:29] Found vcfuniq - /usr/local/bin/vcfuniq
[07:33:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:33:29] Found gzip - /bin/gzip
[07:33:29] Found vt - /usr/local/bin/vt
[07:33:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:33:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:33:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:33:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:33:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:33:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:33:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:33:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:34:10] This is snippy 4.6.0Show full stderr[07:34:10] This is snippy 4.6.0
[07:34:10] Written by Torsten Seemann
[07:34:10] Obtained from https://github.com/tseemann/snippy
[07:34:10] Detected operating system: linux
[07:34:10] Enabling bundled linux tools.
[07:34:10] Found bwa - /usr/local/bin/bwa
[07:34:10] Found bcftools - /usr/local/bin/bcftools
[07:34:10] Found samtools - /usr/local/bin/samtools
[07:34:10] Found java - /usr/local/bin/java
[07:34:10] Found snpEff - /usr/local/bin/snpEff
[07:34:10] Found samclip - /usr/local/bin/samclip
[07:34:10] Found seqtk - /usr/local/bin/seqtk
[07:34:10] Found parallel - /usr/local/bin/parallel
[07:34:10] Found freebayes - /usr/local/bin/freebayes
[07:34:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:34:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:34:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:34:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:34:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:34:10] Found gzip - /bin/gzip
[07:34:10] Found vt - /usr/local/bin/vt
[07:34:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:34:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:34:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:34:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:34:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:34:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:34:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:34:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:34:13] This is snippy 4.6.0Show full stderr[07:34:13] This is snippy 4.6.0
[07:34:13] Written by Torsten Seemann
[07:34:13] Obtained from https://github.com/tseemann/snippy
[07:34:13] Detected operating system: linux
[07:34:13] Enabling bundled linux tools.
[07:34:13] Found bwa - /usr/local/bin/bwa
[07:34:13] Found bcftools - /usr/local/bin/bcftools
[07:34:13] Found samtools - /usr/local/bin/samtools
[07:34:13] Found java - /usr/local/bin/java
[07:34:13] Found snpEff - /usr/local/bin/snpEff
[07:34:13] Found samclip - /usr/local/bin/samclip
[07:34:13] Found seqtk - /usr/local/bin/seqtk
[07:34:13] Found parallel - /usr/local/bin/parallel
[07:34:13] Found freebayes - /usr/local/bin/freebayes
[07:34:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:34:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:34:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:34:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:34:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:34:13] Found gzip - /bin/gzip
[07:34:13] Found vt - /usr/local/bin/vt
[07:34:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:34:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:34:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:34:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:34:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:34:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:34:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:34:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:34:58] This is snippy 4.6.0Show full stderr[07:34:58] This is snippy 4.6.0
[07:34:58] Written by Torsten Seemann
[07:34:58] Obtained from https://github.com/tseemann/snippy
[07:34:58] Detected operating system: linux
[07:34:58] Enabling bundled linux tools.
[07:34:58] Found bwa - /usr/local/bin/bwa
[07:34:58] Found bcftools - /usr/local/bin/bcftools
[07:34:58] Found samtools - /usr/local/bin/samtools
[07:34:58] Found java - /usr/local/bin/java
[07:34:58] Found snpEff - /usr/local/bin/snpEff
[07:34:58] Found samclip - /usr/local/bin/samclip
[07:34:58] Found seqtk - /usr/local/bin/seqtk
[07:34:58] Found parallel - /usr/local/bin/parallel
[07:34:58] Found freebayes - /usr/local/bin/freebayes
[07:34:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:34:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:34:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:34:58] Found vcfuniq - /usr/local/bin/vcfuniq
[07:34:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:34:58] Found gzip - /bin/gzip
[07:34:58] Found vt - /usr/local/bin/vt
[07:34:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:34:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:34:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:34:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:34:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:34:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:34:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:34:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:16] This is snippy 4.6.0Show full stderr[07:36:16] This is snippy 4.6.0
[07:36:16] Written by Torsten Seemann
[07:36:16] Obtained from https://github.com/tseemann/snippy
[07:36:16] Detected operating system: linux
[07:36:16] Enabling bundled linux tools.
[07:36:16] Found bwa - /usr/local/bin/bwa
[07:36:16] Found bcftools - /usr/local/bin/bcftools
[07:36:16] Found samtools - /usr/local/bin/samtools
[07:36:16] Found java - /usr/local/bin/java
[07:36:16] Found snpEff - /usr/local/bin/snpEff
[07:36:16] Found samclip - /usr/local/bin/samclip
[07:36:16] Found seqtk - /usr/local/bin/seqtk
[07:36:16] Found parallel - /usr/local/bin/parallel
[07:36:16] Found freebayes - /usr/local/bin/freebayes
[07:36:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:16] Found gzip - /bin/gzip
[07:36:16] Found vt - /usr/local/bin/vt
[07:36:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:22] This is snippy 4.6.0Show full stderr[07:36:22] This is snippy 4.6.0
[07:36:22] Written by Torsten Seemann
[07:36:22] Obtained from https://github.com/tseemann/snippy
[07:36:22] Detected operating system: linux
[07:36:22] Enabling bundled linux tools.
[07:36:22] Found bwa - /usr/local/bin/bwa
[07:36:22] Found bcftools - /usr/local/bin/bcftools
[07:36:22] Found samtools - /usr/local/bin/samtools
[07:36:22] Found java - /usr/local/bin/java
[07:36:22] Found snpEff - /usr/local/bin/snpEff
[07:36:22] Found samclip - /usr/local/bin/samclip
[07:36:22] Found seqtk - /usr/local/bin/seqtk
[07:36:22] Found parallel - /usr/local/bin/parallel
[07:36:22] Found freebayes - /usr/local/bin/freebayes
[07:36:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:22] Found gzip - /bin/gzip
[07:36:22] Found vt - /usr/local/bin/vt
[07:36:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:37:31] This is snippy 4.6.0Show full stderr[07:37:31] This is snippy 4.6.0
[07:37:31] Written by Torsten Seemann
[07:37:31] Obtained from https://github.com/tseemann/snippy
[07:37:31] Detected operating system: linux
[07:37:31] Enabling bundled linux tools.
[07:37:31] Found bwa - /usr/local/bin/bwa
[07:37:31] Found bcftools - /usr/local/bin/bcftools
[07:37:31] Found samtools - /usr/local/bin/samtools
[07:37:31] Found java - /usr/local/bin/java
[07:37:31] Found snpEff - /usr/local/bin/snpEff
[07:37:31] Found samclip - /usr/local/bin/samclip
[07:37:31] Found seqtk - /usr/local/bin/seqtk
[07:37:31] Found parallel - /usr/local/bin/parallel
[07:37:31] Found freebayes - /usr/local/bin/freebayes
[07:37:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:37:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:37:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:37:31] Found vcfuniq - /usr/local/bin/vcfuniq
[07:37:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:37:31] Found gzip - /bin/gzip
[07:37:31] Found vt - /usr/local/bin/vt
[07:37:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:37:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:37:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:37:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:37:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:37:55] This is snippy 4.6.0Show full stderr[07:37:55] This is snippy 4.6.0
[07:37:55] Written by Torsten Seemann
[07:37:55] Obtained from https://github.com/tseemann/snippy
[07:37:55] Detected operating system: linux
[07:37:55] Enabling bundled linux tools.
[07:37:55] Found bwa - /usr/local/bin/bwa
[07:37:55] Found bcftools - /usr/local/bin/bcftools
[07:37:55] Found samtools - /usr/local/bin/samtools
[07:37:55] Found java - /usr/local/bin/java
[07:37:55] Found snpEff - /usr/local/bin/snpEff
[07:37:55] Found samclip - /usr/local/bin/samclip
[07:37:55] Found seqtk - /usr/local/bin/seqtk
[07:37:55] Found parallel - /usr/local/bin/parallel
[07:37:55] Found freebayes - /usr/local/bin/freebayes
[07:37:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:37:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:37:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:37:55] Found vcfuniq - /usr/local/bin/vcfuniq
[07:37:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:37:55] Found gzip - /bin/gzip
[07:37:55] Found vt - /usr/local/bin/vt
[07:37:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:37:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:37:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:37:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:37:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:38:07] This is snippy 4.6.0Show full stderr[07:38:07] This is snippy 4.6.0
[07:38:07] Written by Torsten Seemann
[07:38:07] Obtained from https://github.com/tseemann/snippy
[07:38:07] Detected operating system: linux
[07:38:07] Enabling bundled linux tools.
[07:38:07] Found bwa - /usr/local/bin/bwa
[07:38:07] Found bcftools - /usr/local/bin/bcftools
[07:38:07] Found samtools - /usr/local/bin/samtools
[07:38:07] Found java - /usr/local/bin/java
[07:38:07] Found snpEff - /usr/local/bin/snpEff
[07:38:07] Found samclip - /usr/local/bin/samclip
[07:38:07] Found seqtk - /usr/local/bin/seqtk
[07:38:07] Found parallel - /usr/local/bin/parallel
[07:38:07] Found freebayes - /usr/local/bin/freebayes
[07:38:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:07] Found gzip - /bin/gzip
[07:38:07] Found vt - /usr/local/bin/vt
[07:38:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:31:13] This is snippy 4.6.0Show full stderr[07:31:13] This is snippy 4.6.0
[07:31:13] Written by Torsten Seemann
[07:31:13] Obtained from https://github.com/tseemann/snippy
[07:31:13] Detected operating system: linux
[07:31:13] Enabling bundled linux tools.
[07:31:13] Found bwa - /usr/local/bin/bwa
[07:31:13] Found bcftools - /usr/local/bin/bcftools
[07:31:13] Found samtools - /usr/local/bin/samtools
[07:31:13] Found java - /usr/local/bin/java
[07:31:13] Found snpEff - /usr/local/bin/snpEff
[07:31:13] Found samclip - /usr/local/bin/samclip
[07:31:13] Found seqtk - /usr/local/bin/seqtk
[07:31:13] Found parallel - /usr/local/bin/parallel
[07:31:13] Found freebayes - /usr/local/bin/freebayes
[07:31:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:31:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:31:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:31:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:31:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:31:13] Found gzip - /bin/gzip
[07:31:13] Found vt - /usr/local/bin/vt
[07:31:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:31:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:31:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:31:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:31:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:31:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:31:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:31:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:31:32] This is snippy 4.6.0Show full stderr[07:31:32] This is snippy 4.6.0
[07:31:32] Written by Torsten Seemann
[07:31:32] Obtained from https://github.com/tseemann/snippy
[07:31:32] Detected operating system: linux
[07:31:32] Enabling bundled linux tools.
[07:31:32] Found bwa - /usr/local/bin/bwa
[07:31:32] Found bcftools - /usr/local/bin/bcftools
[07:31:32] Found samtools - /usr/local/bin/samtools
[07:31:32] Found java - /usr/local/bin/java
[07:31:32] Found snpEff - /usr/local/bin/snpEff
[07:31:32] Found samclip - /usr/local/bin/samclip
[07:31:32] Found seqtk - /usr/local/bin/seqtk
[07:31:32] Found parallel - /usr/local/bin/parallel
[07:31:32] Found freebayes - /usr/local/bin/freebayes
[07:31:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:31:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:31:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:31:32] Found vcfuniq - /usr/local/bin/vcfuniq
[07:31:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:31:32] Found gzip - /bin/gzip
[07:31:32] Found vt - /usr/local/bin/vt
[07:31:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:31:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:31:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:31:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:31:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:31:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:31:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:31:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:31:44] This is snippy 4.6.0Show full stderr[07:31:44] This is snippy 4.6.0
[07:31:44] Written by Torsten Seemann
[07:31:44] Obtained from https://github.com/tseemann/snippy
[07:31:44] Detected operating system: linux
[07:31:44] Enabling bundled linux tools.
[07:31:44] Found bwa - /usr/local/bin/bwa
[07:31:44] Found bcftools - /usr/local/bin/bcftools
[07:31:44] Found samtools - /usr/local/bin/samtools
[07:31:44] Found java - /usr/local/bin/java
[07:31:44] Found snpEff - /usr/local/bin/snpEff
[07:31:44] Found samclip - /usr/local/bin/samclip
[07:31:44] Found seqtk - /usr/local/bin/seqtk
[07:31:44] Found parallel - /usr/local/bin/parallel
[07:31:44] Found freebayes - /usr/local/bin/freebayes
[07:31:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:31:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:31:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:31:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:31:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:31:44] Found gzip - /bin/gzip
[07:31:44] Found vt - /usr/local/bin/vt
[07:31:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:31:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:31:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:31:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:31:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:31:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:31:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:31:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:32:36] This is snippy 4.6.0Show full stderr[07:32:36] This is snippy 4.6.0
[07:32:36] Written by Torsten Seemann
[07:32:36] Obtained from https://github.com/tseemann/snippy
[07:32:36] Detected operating system: linux
[07:32:36] Enabling bundled linux tools.
[07:32:36] Found bwa - /usr/local/bin/bwa
[07:32:36] Found bcftools - /usr/local/bin/bcftools
[07:32:36] Found samtools - /usr/local/bin/samtools
[07:32:36] Found java - /usr/local/bin/java
[07:32:36] Found snpEff - /usr/local/bin/snpEff
[07:32:36] Found samclip - /usr/local/bin/samclip
[07:32:36] Found seqtk - /usr/local/bin/seqtk
[07:32:36] Found parallel - /usr/local/bin/parallel
[07:32:36] Found freebayes - /usr/local/bin/freebayes
[07:32:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:32:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:32:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:32:36] Found vcfuniq - /usr/local/bin/vcfuniq
[07:32:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:32:36] Found gzip - /bin/gzip
[07:32:36] Found vt - /usr/local/bin/vt
[07:32:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:32:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:32:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:32:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:32:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:32:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:32:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:32:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:33:17] This is snippy 4.6.0Show full stderr[07:33:17] This is snippy 4.6.0
[07:33:17] Written by Torsten Seemann
[07:33:17] Obtained from https://github.com/tseemann/snippy
[07:33:17] Detected operating system: linux
[07:33:17] Enabling bundled linux tools.
[07:33:17] Found bwa - /usr/local/bin/bwa
[07:33:17] Found bcftools - /usr/local/bin/bcftools
[07:33:17] Found samtools - /usr/local/bin/samtools
[07:33:17] Found java - /usr/local/bin/java
[07:33:17] Found snpEff - /usr/local/bin/snpEff
[07:33:17] Found samclip - /usr/local/bin/samclip
[07:33:17] Found seqtk - /usr/local/bin/seqtk
[07:33:17] Found parallel - /usr/local/bin/parallel
[07:33:17] Found freebayes - /usr/local/bin/freebayes
[07:33:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:33:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:33:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:33:17] Found vcfuniq - /usr/local/bin/vcfuniq
[07:33:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:33:17] Found gzip - /bin/gzip
[07:33:17] Found vt - /usr/local/bin/vt
[07:33:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:33:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:33:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:33:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:33:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:33:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:33:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:33:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:13] This is snippy 4.6.0Show full stderr[07:36:13] This is snippy 4.6.0
[07:36:13] Written by Torsten Seemann
[07:36:13] Obtained from https://github.com/tseemann/snippy
[07:36:13] Detected operating system: linux
[07:36:13] Enabling bundled linux tools.
[07:36:13] Found bwa - /usr/local/bin/bwa
[07:36:13] Found bcftools - /usr/local/bin/bcftools
[07:36:13] Found samtools - /usr/local/bin/samtools
[07:36:13] Found java - /usr/local/bin/java
[07:36:13] Found snpEff - /usr/local/bin/snpEff
[07:36:13] Found samclip - /usr/local/bin/samclip
[07:36:13] Found seqtk - /usr/local/bin/seqtk
[07:36:13] Found parallel - /usr/local/bin/parallel
[07:36:13] Found freebayes - /usr/local/bin/freebayes
[07:36:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:13] Found gzip - /bin/gzip
[07:36:13] Found vt - /usr/local/bin/vt
[07:36:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:28] This is snippy 4.6.0Show full stderr[07:36:28] This is snippy 4.6.0
[07:36:28] Written by Torsten Seemann
[07:36:28] Obtained from https://github.com/tseemann/snippy
[07:36:28] Detected operating system: linux
[07:36:28] Enabling bundled linux tools.
[07:36:28] Found bwa - /usr/local/bin/bwa
[07:36:28] Found bcftools - /usr/local/bin/bcftools
[07:36:28] Found samtools - /usr/local/bin/samtools
[07:36:28] Found java - /usr/local/bin/java
[07:36:28] Found snpEff - /usr/local/bin/snpEff
[07:36:28] Found samclip - /usr/local/bin/samclip
[07:36:28] Found seqtk - /usr/local/bin/seqtk
[07:36:28] Found parallel - /usr/local/bin/parallel
[07:36:28] Found freebayes - /usr/local/bin/freebayes
[07:36:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:28] Found gzip - /bin/gzip
[07:36:28] Found vt - /usr/local/bin/vt
[07:36:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:41] This is snippy 4.6.0Show full stderr[07:36:41] This is snippy 4.6.0
[07:36:41] Written by Torsten Seemann
[07:36:41] Obtained from https://github.com/tseemann/snippy
[07:36:41] Detected operating system: linux
[07:36:41] Enabling bundled linux tools.
[07:36:41] Found bwa - /usr/local/bin/bwa
[07:36:41] Found bcftools - /usr/local/bin/bcftools
[07:36:41] Found samtools - /usr/local/bin/samtools
[07:36:41] Found java - /usr/local/bin/java
[07:36:41] Found snpEff - /usr/local/bin/snpEff
[07:36:41] Found samclip - /usr/local/bin/samclip
[07:36:41] Found seqtk - /usr/local/bin/seqtk
[07:36:41] Found parallel - /usr/local/bin/parallel
[07:36:41] Found freebayes - /usr/local/bin/freebayes
[07:36:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:41] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:41] Found gzip - /bin/gzip
[07:36:41] Found vt - /usr/local/bin/vt
[07:36:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:59] This is snippy 4.6.0Show full stderr[07:36:59] This is snippy 4.6.0
[07:36:59] Written by Torsten Seemann
[07:36:59] Obtained from https://github.com/tseemann/snippy
[07:36:59] Detected operating system: linux
[07:36:59] Enabling bundled linux tools.
[07:36:59] Found bwa - /usr/local/bin/bwa
[07:36:59] Found bcftools - /usr/local/bin/bcftools
[07:36:59] Found samtools - /usr/local/bin/samtools
[07:36:59] Found java - /usr/local/bin/java
[07:36:59] Found snpEff - /usr/local/bin/snpEff
[07:36:59] Found samclip - /usr/local/bin/samclip
[07:36:59] Found seqtk - /usr/local/bin/seqtk
[07:36:59] Found parallel - /usr/local/bin/parallel
[07:36:59] Found freebayes - /usr/local/bin/freebayes
[07:36:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:59] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:59] Found gzip - /bin/gzip
[07:36:59] Found vt - /usr/local/bin/vt
[07:36:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:37:10] This is snippy 4.6.0Show full stderr[07:37:10] This is snippy 4.6.0
[07:37:10] Written by Torsten Seemann
[07:37:10] Obtained from https://github.com/tseemann/snippy
[07:37:10] Detected operating system: linux
[07:37:10] Enabling bundled linux tools.
[07:37:10] Found bwa - /usr/local/bin/bwa
[07:37:10] Found bcftools - /usr/local/bin/bcftools
[07:37:10] Found samtools - /usr/local/bin/samtools
[07:37:10] Found java - /usr/local/bin/java
[07:37:10] Found snpEff - /usr/local/bin/snpEff
[07:37:10] Found samclip - /usr/local/bin/samclip
[07:37:10] Found seqtk - /usr/local/bin/seqtk
[07:37:10] Found parallel - /usr/local/bin/parallel
[07:37:10] Found freebayes - /usr/local/bin/freebayes
[07:37:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:37:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:37:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:37:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:37:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:37:10] Found gzip - /bin/gzip
[07:37:10] Found vt - /usr/local/bin/vt
[07:37:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:37:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:37:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:37:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:37:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:37:13] This is snippy 4.6.0Show full stderr[07:37:13] This is snippy 4.6.0
[07:37:13] Written by Torsten Seemann
[07:37:13] Obtained from https://github.com/tseemann/snippy
[07:37:13] Detected operating system: linux
[07:37:13] Enabling bundled linux tools.
[07:37:13] Found bwa - /usr/local/bin/bwa
[07:37:13] Found bcftools - /usr/local/bin/bcftools
[07:37:13] Found samtools - /usr/local/bin/samtools
[07:37:13] Found java - /usr/local/bin/java
[07:37:13] Found snpEff - /usr/local/bin/snpEff
[07:37:13] Found samclip - /usr/local/bin/samclip
[07:37:13] Found seqtk - /usr/local/bin/seqtk
[07:37:13] Found parallel - /usr/local/bin/parallel
[07:37:13] Found freebayes - /usr/local/bin/freebayes
[07:37:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:37:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:37:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:37:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:37:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:37:13] Found gzip - /bin/gzip
[07:37:13] Found vt - /usr/local/bin/vt
[07:37:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:37:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:37:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:37:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:37:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:37:40] This is snippy 4.6.0Show full stderr[07:37:40] This is snippy 4.6.0
[07:37:40] Written by Torsten Seemann
[07:37:40] Obtained from https://github.com/tseemann/snippy
[07:37:40] Detected operating system: linux
[07:37:40] Enabling bundled linux tools.
[07:37:40] Found bwa - /usr/local/bin/bwa
[07:37:40] Found bcftools - /usr/local/bin/bcftools
[07:37:40] Found samtools - /usr/local/bin/samtools
[07:37:40] Found java - /usr/local/bin/java
[07:37:40] Found snpEff - /usr/local/bin/snpEff
[07:37:40] Found samclip - /usr/local/bin/samclip
[07:37:40] Found seqtk - /usr/local/bin/seqtk
[07:37:40] Found parallel - /usr/local/bin/parallel
[07:37:40] Found freebayes - /usr/local/bin/freebayes
[07:37:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:37:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:37:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:37:40] Found vcfuniq - /usr/local/bin/vcfuniq
[07:37:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:37:40] Found gzip - /bin/gzip
[07:37:40] Found vt - /usr/local/bin/vt
[07:37:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:37:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:37:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:37:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:37:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:38:22] This is snippy 4.6.0Show full stderr[07:38:22] This is snippy 4.6.0
[07:38:22] Written by Torsten Seemann
[07:38:22] Obtained from https://github.com/tseemann/snippy
[07:38:22] Detected operating system: linux
[07:38:22] Enabling bundled linux tools.
[07:38:22] Found bwa - /usr/local/bin/bwa
[07:38:22] Found bcftools - /usr/local/bin/bcftools
[07:38:22] Found samtools - /usr/local/bin/samtools
[07:38:22] Found java - /usr/local/bin/java
[07:38:22] Found snpEff - /usr/local/bin/snpEff
[07:38:22] Found samclip - /usr/local/bin/samclip
[07:38:22] Found seqtk - /usr/local/bin/seqtk
[07:38:22] Found parallel - /usr/local/bin/parallel
[07:38:22] Found freebayes - /usr/local/bin/freebayes
[07:38:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:22] Found gzip - /bin/gzip
[07:38:22] Found vt - /usr/local/bin/vt
[07:38:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:35:27] This is snippy 4.6.0Show full stderr[07:35:27] This is snippy 4.6.0
[07:35:27] Written by Torsten Seemann
[07:35:27] Obtained from https://github.com/tseemann/snippy
[07:35:27] Detected operating system: linux
[07:35:27] Enabling bundled linux tools.
[07:35:27] Found bwa - /usr/local/bin/bwa
[07:35:27] Found bcftools - /usr/local/bin/bcftools
[07:35:27] Found samtools - /usr/local/bin/samtools
[07:35:27] Found java - /usr/local/bin/java
[07:35:27] Found snpEff - /usr/local/bin/snpEff
[07:35:27] Found samclip - /usr/local/bin/samclip
[07:35:27] Found seqtk - /usr/local/bin/seqtk
[07:35:27] Found parallel - /usr/local/bin/parallel
[07:35:27] Found freebayes - /usr/local/bin/freebayes
[07:35:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:35:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:35:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:35:27] Found vcfuniq - /usr/local/bin/vcfuniq
[07:35:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:35:27] Found gzip - /bin/gzip
[07:35:27] Found vt - /usr/local/bin/vt
[07:35:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:35:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:35:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:35:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:35:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:35:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:35:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:35:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:00] This is snippy 4.6.0Show full stderr[07:36:00] This is snippy 4.6.0
[07:36:00] Written by Torsten Seemann
[07:36:00] Obtained from https://github.com/tseemann/snippy
[07:36:00] Detected operating system: linux
[07:36:00] Enabling bundled linux tools.
[07:36:00] Found bwa - /usr/local/bin/bwa
[07:36:00] Found bcftools - /usr/local/bin/bcftools
[07:36:00] Found samtools - /usr/local/bin/samtools
[07:36:00] Found java - /usr/local/bin/java
[07:36:00] Found snpEff - /usr/local/bin/snpEff
[07:36:00] Found samclip - /usr/local/bin/samclip
[07:36:00] Found seqtk - /usr/local/bin/seqtk
[07:36:00] Found parallel - /usr/local/bin/parallel
[07:36:00] Found freebayes - /usr/local/bin/freebayes
[07:36:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:00] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:00] Found gzip - /bin/gzip
[07:36:00] Found vt - /usr/local/bin/vt
[07:36:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:03] This is snippy 4.6.0Show full stderr[07:36:03] This is snippy 4.6.0
[07:36:03] Written by Torsten Seemann
[07:36:03] Obtained from https://github.com/tseemann/snippy
[07:36:03] Detected operating system: linux
[07:36:03] Enabling bundled linux tools.
[07:36:03] Found bwa - /usr/local/bin/bwa
[07:36:03] Found bcftools - /usr/local/bin/bcftools
[07:36:03] Found samtools - /usr/local/bin/samtools
[07:36:03] Found java - /usr/local/bin/java
[07:36:03] Found snpEff - /usr/local/bin/snpEff
[07:36:03] Found samclip - /usr/local/bin/samclip
[07:36:03] Found seqtk - /usr/local/bin/seqtk
[07:36:03] Found parallel - /usr/local/bin/parallel
[07:36:03] Found freebayes - /usr/local/bin/freebayes
[07:36:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:03] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:03] Found gzip - /bin/gzip
[07:36:03] Found vt - /usr/local/bin/vt
[07:36:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:37:25] This is snippy 4.6.0Show full stderr[07:37:25] This is snippy 4.6.0
[07:37:25] Written by Torsten Seemann
[07:37:25] Obtained from https://github.com/tseemann/snippy
[07:37:25] Detected operating system: linux
[07:37:25] Enabling bundled linux tools.
[07:37:25] Found bwa - /usr/local/bin/bwa
[07:37:25] Found bcftools - /usr/local/bin/bcftools
[07:37:25] Found samtools - /usr/local/bin/samtools
[07:37:25] Found java - /usr/local/bin/java
[07:37:25] Found snpEff - /usr/local/bin/snpEff
[07:37:25] Found samclip - /usr/local/bin/samclip
[07:37:25] Found seqtk - /usr/local/bin/seqtk
[07:37:25] Found parallel - /usr/local/bin/parallel
[07:37:25] Found freebayes - /usr/local/bin/freebayes
[07:37:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:37:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:37:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:37:25] Found vcfuniq - /usr/local/bin/vcfuniq
[07:37:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:37:25] Found gzip - /bin/gzip
[07:37:25] Found vt - /usr/local/bin/vt
[07:37:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:37:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:37:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:37:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:37:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:37:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:37:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:37:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:38:36] This is snippy 4.6.0Show full stderr[07:38:36] This is snippy 4.6.0
[07:38:36] Written by Torsten Seemann
[07:38:36] Obtained from https://github.com/tseemann/snippy
[07:38:36] Detected operating system: linux
[07:38:36] Enabling bundled linux tools.
[07:38:36] Found bwa - /usr/local/bin/bwa
[07:38:36] Found bcftools - /usr/local/bin/bcftools
[07:38:36] Found samtools - /usr/local/bin/samtools
[07:38:36] Found java - /usr/local/bin/java
[07:38:36] Found snpEff - /usr/local/bin/snpEff
[07:38:36] Found samclip - /usr/local/bin/samclip
[07:38:36] Found seqtk - /usr/local/bin/seqtk
[07:38:36] Found parallel - /usr/local/bin/parallel
[07:38:36] Found freebayes - /usr/local/bin/freebayes
[07:38:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:36] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:36] Found gzip - /bin/gzip
[07:38:36] Found vt - /usr/local/bin/vt
[07:38:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:38:57] This is snippy 4.6.0Show full stderr[07:38:57] This is snippy 4.6.0
[07:38:57] Written by Torsten Seemann
[07:38:57] Obtained from https://github.com/tseemann/snippy
[07:38:57] Detected operating system: linux
[07:38:57] Enabling bundled linux tools.
[07:38:57] Found bwa - /usr/local/bin/bwa
[07:38:57] Found bcftools - /usr/local/bin/bcftools
[07:38:58] Found samtools - /usr/local/bin/samtools
[07:38:58] Found java - /usr/local/bin/java
[07:38:58] Found snpEff - /usr/local/bin/snpEff
[07:38:58] Found samclip - /usr/local/bin/samclip
[07:38:58] Found seqtk - /usr/local/bin/seqtk
[07:38:58] Found parallel - /usr/local/bin/parallel
[07:38:58] Found freebayes - /usr/local/bin/freebayes
[07:38:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:58] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:58] Found gzip - /bin/gzip
[07:38:58] Found vt - /usr/local/bin/vt
[07:38:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:40:44] This is snippy 4.6.0Show full stderr[07:40:44] This is snippy 4.6.0
[07:40:44] Written by Torsten Seemann
[07:40:44] Obtained from https://github.com/tseemann/snippy
[07:40:44] Detected operating system: linux
[07:40:44] Enabling bundled linux tools.
[07:40:44] Found bwa - /usr/local/bin/bwa
[07:40:44] Found bcftools - /usr/local/bin/bcftools
[07:40:44] Found samtools - /usr/local/bin/samtools
[07:40:44] Found java - /usr/local/bin/java
[07:40:44] Found snpEff - /usr/local/bin/snpEff
[07:40:44] Found samclip - /usr/local/bin/samclip
[07:40:44] Found seqtk - /usr/local/bin/seqtk
[07:40:44] Found parallel - /usr/local/bin/parallel
[07:40:44] Found freebayes - /usr/local/bin/freebayes
[07:40:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:44] Found gzip - /bin/gzip
[07:40:44] Found vt - /usr/local/bin/vt
[07:40:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:39:51] This is snippy 4.6.0Show full stderr[07:39:51] This is snippy 4.6.0
[07:39:51] Written by Torsten Seemann
[07:39:51] Obtained from https://github.com/tseemann/snippy
[07:39:51] Detected operating system: linux
[07:39:51] Enabling bundled linux tools.
[07:39:51] Found bwa - /usr/local/bin/bwa
[07:39:51] Found bcftools - /usr/local/bin/bcftools
[07:39:51] Found samtools - /usr/local/bin/samtools
[07:39:51] Found java - /usr/local/bin/java
[07:39:51] Found snpEff - /usr/local/bin/snpEff
[07:39:51] Found samclip - /usr/local/bin/samclip
[07:39:51] Found seqtk - /usr/local/bin/seqtk
[07:39:51] Found parallel - /usr/local/bin/parallel
[07:39:51] Found freebayes - /usr/local/bin/freebayes
[07:39:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:39:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:39:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:39:51] Found vcfuniq - /usr/local/bin/vcfuniq
[07:39:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:39:51] Found gzip - /bin/gzip
[07:39:51] Found vt - /usr/local/bin/vt
[07:39:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:39:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:39:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:39:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:39:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:39:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:39:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:39:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:40:03] This is snippy 4.6.0Show full stderr[07:40:03] This is snippy 4.6.0
[07:40:03] Written by Torsten Seemann
[07:40:03] Obtained from https://github.com/tseemann/snippy
[07:40:03] Detected operating system: linux
[07:40:03] Enabling bundled linux tools.
[07:40:03] Found bwa - /usr/local/bin/bwa
[07:40:03] Found bcftools - /usr/local/bin/bcftools
[07:40:03] Found samtools - /usr/local/bin/samtools
[07:40:03] Found java - /usr/local/bin/java
[07:40:03] Found snpEff - /usr/local/bin/snpEff
[07:40:03] Found samclip - /usr/local/bin/samclip
[07:40:03] Found seqtk - /usr/local/bin/seqtk
[07:40:03] Found parallel - /usr/local/bin/parallel
[07:40:03] Found freebayes - /usr/local/bin/freebayes
[07:40:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:04] Found gzip - /bin/gzip
[07:40:04] Found vt - /usr/local/bin/vt
[07:40:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:40:15] This is snippy 4.6.0Show full stderr[07:40:15] This is snippy 4.6.0
[07:40:15] Written by Torsten Seemann
[07:40:15] Obtained from https://github.com/tseemann/snippy
[07:40:15] Detected operating system: linux
[07:40:15] Enabling bundled linux tools.
[07:40:15] Found bwa - /usr/local/bin/bwa
[07:40:15] Found bcftools - /usr/local/bin/bcftools
[07:40:15] Found samtools - /usr/local/bin/samtools
[07:40:15] Found java - /usr/local/bin/java
[07:40:15] Found snpEff - /usr/local/bin/snpEff
[07:40:15] Found samclip - /usr/local/bin/samclip
[07:40:15] Found seqtk - /usr/local/bin/seqtk
[07:40:15] Found parallel - /usr/local/bin/parallel
[07:40:15] Found freebayes - /usr/local/bin/freebayes
[07:40:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:15] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:16] Found gzip - /bin/gzip
[07:40:16] Found vt - /usr/local/bin/vt
[07:40:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:40:58] This is snippy 4.6.0Show full stderr[07:40:58] This is snippy 4.6.0
[07:40:58] Written by Torsten Seemann
[07:40:58] Obtained from https://github.com/tseemann/snippy
[07:40:58] Detected operating system: linux
[07:40:58] Enabling bundled linux tools.
[07:40:58] Found bwa - /usr/local/bin/bwa
[07:40:58] Found bcftools - /usr/local/bin/bcftools
[07:40:58] Found samtools - /usr/local/bin/samtools
[07:40:58] Found java - /usr/local/bin/java
[07:40:58] Found snpEff - /usr/local/bin/snpEff
[07:40:58] Found samclip - /usr/local/bin/samclip
[07:40:58] Found seqtk - /usr/local/bin/seqtk
[07:40:58] Found parallel - /usr/local/bin/parallel
[07:40:58] Found freebayes - /usr/local/bin/freebayes
[07:40:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:58] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:58] Found gzip - /bin/gzip
[07:40:58] Found vt - /usr/local/bin/vt
[07:40:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:42:22] This is snippy 4.6.0Show full stderr[07:42:22] This is snippy 4.6.0
[07:42:22] Written by Torsten Seemann
[07:42:22] Obtained from https://github.com/tseemann/snippy
[07:42:22] Detected operating system: linux
[07:42:22] Enabling bundled linux tools.
[07:42:22] Found bwa - /usr/local/bin/bwa
[07:42:22] Found bcftools - /usr/local/bin/bcftools
[07:42:22] Found samtools - /usr/local/bin/samtools
[07:42:22] Found java - /usr/local/bin/java
[07:42:22] Found snpEff - /usr/local/bin/snpEff
[07:42:22] Found samclip - /usr/local/bin/samclip
[07:42:22] Found seqtk - /usr/local/bin/seqtk
[07:42:22] Found parallel - /usr/local/bin/parallel
[07:42:22] Found freebayes - /usr/local/bin/freebayes
[07:42:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:22] Found gzip - /bin/gzip
[07:42:22] Found vt - /usr/local/bin/vt
[07:42:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:42:28] This is snippy 4.6.0Show full stderr[07:42:28] This is snippy 4.6.0
[07:42:28] Written by Torsten Seemann
[07:42:28] Obtained from https://github.com/tseemann/snippy
[07:42:28] Detected operating system: linux
[07:42:28] Enabling bundled linux tools.
[07:42:28] Found bwa - /usr/local/bin/bwa
[07:42:28] Found bcftools - /usr/local/bin/bcftools
[07:42:28] Found samtools - /usr/local/bin/samtools
[07:42:28] Found java - /usr/local/bin/java
[07:42:28] Found snpEff - /usr/local/bin/snpEff
[07:42:28] Found samclip - /usr/local/bin/samclip
[07:42:28] Found seqtk - /usr/local/bin/seqtk
[07:42:28] Found parallel - /usr/local/bin/parallel
[07:42:28] Found freebayes - /usr/local/bin/freebayes
[07:42:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:28] Found gzip - /bin/gzip
[07:42:28] Found vt - /usr/local/bin/vt
[07:42:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:42:31] This is snippy 4.6.0Show full stderr[07:42:31] This is snippy 4.6.0
[07:42:31] Written by Torsten Seemann
[07:42:31] Obtained from https://github.com/tseemann/snippy
[07:42:31] Detected operating system: linux
[07:42:31] Enabling bundled linux tools.
[07:42:31] Found bwa - /usr/local/bin/bwa
[07:42:31] Found bcftools - /usr/local/bin/bcftools
[07:42:31] Found samtools - /usr/local/bin/samtools
[07:42:31] Found java - /usr/local/bin/java
[07:42:31] Found snpEff - /usr/local/bin/snpEff
[07:42:31] Found samclip - /usr/local/bin/samclip
[07:42:31] Found seqtk - /usr/local/bin/seqtk
[07:42:31] Found parallel - /usr/local/bin/parallel
[07:42:31] Found freebayes - /usr/local/bin/freebayes
[07:42:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:31] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:31] Found gzip - /bin/gzip
[07:42:31] Found vt - /usr/local/bin/vt
[07:42:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:34:28] This is snippy 4.6.0Show full stderr[07:34:28] This is snippy 4.6.0
[07:34:28] Written by Torsten Seemann
[07:34:28] Obtained from https://github.com/tseemann/snippy
[07:34:28] Detected operating system: linux
[07:34:28] Enabling bundled linux tools.
[07:34:28] Found bwa - /usr/local/bin/bwa
[07:34:28] Found bcftools - /usr/local/bin/bcftools
[07:34:28] Found samtools - /usr/local/bin/samtools
[07:34:28] Found java - /usr/local/bin/java
[07:34:28] Found snpEff - /usr/local/bin/snpEff
[07:34:28] Found samclip - /usr/local/bin/samclip
[07:34:28] Found seqtk - /usr/local/bin/seqtk
[07:34:28] Found parallel - /usr/local/bin/parallel
[07:34:28] Found freebayes - /usr/local/bin/freebayes
[07:34:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:34:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:34:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:34:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:34:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:34:28] Found gzip - /bin/gzip
[07:34:28] Found vt - /usr/local/bin/vt
[07:34:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:34:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:34:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:34:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:34:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:34:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:34:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:34:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:35:45] This is snippy 4.6.0Show full stderr[07:35:45] This is snippy 4.6.0
[07:35:45] Written by Torsten Seemann
[07:35:45] Obtained from https://github.com/tseemann/snippy
[07:35:45] Detected operating system: linux
[07:35:45] Enabling bundled linux tools.
[07:35:45] Found bwa - /usr/local/bin/bwa
[07:35:45] Found bcftools - /usr/local/bin/bcftools
[07:35:45] Found samtools - /usr/local/bin/samtools
[07:35:45] Found java - /usr/local/bin/java
[07:35:45] Found snpEff - /usr/local/bin/snpEff
[07:35:45] Found samclip - /usr/local/bin/samclip
[07:35:45] Found seqtk - /usr/local/bin/seqtk
[07:35:45] Found parallel - /usr/local/bin/parallel
[07:35:45] Found freebayes - /usr/local/bin/freebayes
[07:35:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:35:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:35:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:35:45] Found vcfuniq - /usr/local/bin/vcfuniq
[07:35:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:35:45] Found gzip - /bin/gzip
[07:35:45] Found vt - /usr/local/bin/vt
[07:35:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:35:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:35:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:35:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:35:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:35:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:35:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:35:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:07] This is snippy 4.6.0Show full stderr[07:36:07] This is snippy 4.6.0
[07:36:07] Written by Torsten Seemann
[07:36:07] Obtained from https://github.com/tseemann/snippy
[07:36:07] Detected operating system: linux
[07:36:07] Enabling bundled linux tools.
[07:36:07] Found bwa - /usr/local/bin/bwa
[07:36:07] Found bcftools - /usr/local/bin/bcftools
[07:36:07] Found samtools - /usr/local/bin/samtools
[07:36:07] Found java - /usr/local/bin/java
[07:36:07] Found snpEff - /usr/local/bin/snpEff
[07:36:07] Found samclip - /usr/local/bin/samclip
[07:36:07] Found seqtk - /usr/local/bin/seqtk
[07:36:07] Found parallel - /usr/local/bin/parallel
[07:36:07] Found freebayes - /usr/local/bin/freebayes
[07:36:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:07] Found gzip - /bin/gzip
[07:36:07] Found vt - /usr/local/bin/vt
[07:36:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:19] This is snippy 4.6.0Show full stderr[07:36:19] This is snippy 4.6.0
[07:36:19] Written by Torsten Seemann
[07:36:19] Obtained from https://github.com/tseemann/snippy
[07:36:19] Detected operating system: linux
[07:36:19] Enabling bundled linux tools.
[07:36:19] Found bwa - /usr/local/bin/bwa
[07:36:19] Found bcftools - /usr/local/bin/bcftools
[07:36:19] Found samtools - /usr/local/bin/samtools
[07:36:19] Found java - /usr/local/bin/java
[07:36:19] Found snpEff - /usr/local/bin/snpEff
[07:36:19] Found samclip - /usr/local/bin/samclip
[07:36:19] Found seqtk - /usr/local/bin/seqtk
[07:36:19] Found parallel - /usr/local/bin/parallel
[07:36:19] Found freebayes - /usr/local/bin/freebayes
[07:36:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:19] Found gzip - /bin/gzip
[07:36:19] Found vt - /usr/local/bin/vt
[07:36:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:31] This is snippy 4.6.0Show full stderr[07:36:31] This is snippy 4.6.0
[07:36:31] Written by Torsten Seemann
[07:36:31] Obtained from https://github.com/tseemann/snippy
[07:36:31] Detected operating system: linux
[07:36:31] Enabling bundled linux tools.
[07:36:31] Found bwa - /usr/local/bin/bwa
[07:36:31] Found bcftools - /usr/local/bin/bcftools
[07:36:31] Found samtools - /usr/local/bin/samtools
[07:36:31] Found java - /usr/local/bin/java
[07:36:31] Found snpEff - /usr/local/bin/snpEff
[07:36:31] Found samclip - /usr/local/bin/samclip
[07:36:31] Found seqtk - /usr/local/bin/seqtk
[07:36:31] Found parallel - /usr/local/bin/parallel
[07:36:31] Found freebayes - /usr/local/bin/freebayes
[07:36:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:31] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:31] Found gzip - /bin/gzip
[07:36:31] Found vt - /usr/local/bin/vt
[07:36:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:44] This is snippy 4.6.0Show full stderr[07:36:44] This is snippy 4.6.0
[07:36:44] Written by Torsten Seemann
[07:36:44] Obtained from https://github.com/tseemann/snippy
[07:36:44] Detected operating system: linux
[07:36:44] Enabling bundled linux tools.
[07:36:44] Found bwa - /usr/local/bin/bwa
[07:36:44] Found bcftools - /usr/local/bin/bcftools
[07:36:44] Found samtools - /usr/local/bin/samtools
[07:36:44] Found java - /usr/local/bin/java
[07:36:44] Found snpEff - /usr/local/bin/snpEff
[07:36:44] Found samclip - /usr/local/bin/samclip
[07:36:44] Found seqtk - /usr/local/bin/seqtk
[07:36:44] Found parallel - /usr/local/bin/parallel
[07:36:44] Found freebayes - /usr/local/bin/freebayes
[07:36:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:44] Found gzip - /bin/gzip
[07:36:44] Found vt - /usr/local/bin/vt
[07:36:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:36:56] This is snippy 4.6.0Show full stderr[07:36:56] This is snippy 4.6.0
[07:36:56] Written by Torsten Seemann
[07:36:56] Obtained from https://github.com/tseemann/snippy
[07:36:56] Detected operating system: linux
[07:36:56] Enabling bundled linux tools.
[07:36:56] Found bwa - /usr/local/bin/bwa
[07:36:56] Found bcftools - /usr/local/bin/bcftools
[07:36:56] Found samtools - /usr/local/bin/samtools
[07:36:56] Found java - /usr/local/bin/java
[07:36:56] Found snpEff - /usr/local/bin/snpEff
[07:36:56] Found samclip - /usr/local/bin/samclip
[07:36:56] Found seqtk - /usr/local/bin/seqtk
[07:36:56] Found parallel - /usr/local/bin/parallel
[07:36:56] Found freebayes - /usr/local/bin/freebayes
[07:36:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:36:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:36:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:36:56] Found vcfuniq - /usr/local/bin/vcfuniq
[07:36:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:36:56] Found gzip - /bin/gzip
[07:36:56] Found vt - /usr/local/bin/vt
[07:36:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:36:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:36:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:36:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:36:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:36:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:36:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:36:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:38:42] This is snippy 4.6.0Show full stderr[07:38:42] This is snippy 4.6.0
[07:38:42] Written by Torsten Seemann
[07:38:42] Obtained from https://github.com/tseemann/snippy
[07:38:42] Detected operating system: linux
[07:38:42] Enabling bundled linux tools.
[07:38:42] Found bwa - /usr/local/bin/bwa
[07:38:42] Found bcftools - /usr/local/bin/bcftools
[07:38:42] Found samtools - /usr/local/bin/samtools
[07:38:42] Found java - /usr/local/bin/java
[07:38:42] Found snpEff - /usr/local/bin/snpEff
[07:38:42] Found samclip - /usr/local/bin/samclip
[07:38:42] Found seqtk - /usr/local/bin/seqtk
[07:38:42] Found parallel - /usr/local/bin/parallel
[07:38:42] Found freebayes - /usr/local/bin/freebayes
[07:38:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:42] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:42] Found gzip - /bin/gzip
[07:38:42] Found vt - /usr/local/bin/vt
[07:38:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:38:51] This is snippy 4.6.0Show full stderr[07:38:51] This is snippy 4.6.0
[07:38:51] Written by Torsten Seemann
[07:38:51] Obtained from https://github.com/tseemann/snippy
[07:38:51] Detected operating system: linux
[07:38:51] Enabling bundled linux tools.
[07:38:51] Found bwa - /usr/local/bin/bwa
[07:38:51] Found bcftools - /usr/local/bin/bcftools
[07:38:51] Found samtools - /usr/local/bin/samtools
[07:38:51] Found java - /usr/local/bin/java
[07:38:51] Found snpEff - /usr/local/bin/snpEff
[07:38:51] Found samclip - /usr/local/bin/samclip
[07:38:51] Found seqtk - /usr/local/bin/seqtk
[07:38:51] Found parallel - /usr/local/bin/parallel
[07:38:51] Found freebayes - /usr/local/bin/freebayes
[07:38:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:51] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:51] Found gzip - /bin/gzip
[07:38:51] Found vt - /usr/local/bin/vt
[07:38:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:39:10] This is snippy 4.6.0Show full stderr[07:39:10] This is snippy 4.6.0
[07:39:10] Written by Torsten Seemann
[07:39:10] Obtained from https://github.com/tseemann/snippy
[07:39:10] Detected operating system: linux
[07:39:10] Enabling bundled linux tools.
[07:39:10] Found bwa - /usr/local/bin/bwa
[07:39:10] Found bcftools - /usr/local/bin/bcftools
[07:39:10] Found samtools - /usr/local/bin/samtools
[07:39:10] Found java - /usr/local/bin/java
[07:39:10] Found snpEff - /usr/local/bin/snpEff
[07:39:10] Found samclip - /usr/local/bin/samclip
[07:39:10] Found seqtk - /usr/local/bin/seqtk
[07:39:10] Found parallel - /usr/local/bin/parallel
[07:39:10] Found freebayes - /usr/local/bin/freebayes
[07:39:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:39:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:39:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:39:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:39:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:39:10] Found gzip - /bin/gzip
[07:39:10] Found vt - /usr/local/bin/vt
[07:39:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:39:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:39:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:39:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:39:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:39:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:39:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:39:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:39:40] This is snippy 4.6.0Show full stderr[07:39:40] This is snippy 4.6.0
[07:39:40] Written by Torsten Seemann
[07:39:40] Obtained from https://github.com/tseemann/snippy
[07:39:40] Detected operating system: linux
[07:39:40] Enabling bundled linux tools.
[07:39:40] Found bwa - /usr/local/bin/bwa
[07:39:40] Found bcftools - /usr/local/bin/bcftools
[07:39:40] Found samtools - /usr/local/bin/samtools
[07:39:40] Found java - /usr/local/bin/java
[07:39:40] Found snpEff - /usr/local/bin/snpEff
[07:39:40] Found samclip - /usr/local/bin/samclip
[07:39:40] Found seqtk - /usr/local/bin/seqtk
[07:39:40] Found parallel - /usr/local/bin/parallel
[07:39:41] Found freebayes - /usr/local/bin/freebayes
[07:39:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:39:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:39:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:39:41] Found vcfuniq - /usr/local/bin/vcfuniq
[07:39:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:39:41] Found gzip - /bin/gzip
[07:39:41] Found vt - /usr/local/bin/vt
[07:39:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:39:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:39:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:39:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:39:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:39:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:39:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:39:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:39:56] This is snippy 4.6.0Show full stderr[07:39:56] This is snippy 4.6.0
[07:39:56] Written by Torsten Seemann
[07:39:56] Obtained from https://github.com/tseemann/snippy
[07:39:56] Detected operating system: linux
[07:39:56] Enabling bundled linux tools.
[07:39:56] Found bwa - /usr/local/bin/bwa
[07:39:56] Found bcftools - /usr/local/bin/bcftools
[07:39:56] Found samtools - /usr/local/bin/samtools
[07:39:56] Found java - /usr/local/bin/java
[07:39:56] Found snpEff - /usr/local/bin/snpEff
[07:39:56] Found samclip - /usr/local/bin/samclip
[07:39:56] Found seqtk - /usr/local/bin/seqtk
[07:39:56] Found parallel - /usr/local/bin/parallel
[07:39:56] Found freebayes - /usr/local/bin/freebayes
[07:39:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:39:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:39:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:39:57] Found vcfuniq - /usr/local/bin/vcfuniq
[07:39:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:39:57] Found gzip - /bin/gzip
[07:39:57] Found vt - /usr/local/bin/vt
[07:39:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:39:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:39:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:39:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:39:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:39:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:39:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:39:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:40:10] This is snippy 4.6.0Show full stderr[07:40:10] This is snippy 4.6.0
[07:40:10] Written by Torsten Seemann
[07:40:10] Obtained from https://github.com/tseemann/snippy
[07:40:10] Detected operating system: linux
[07:40:10] Enabling bundled linux tools.
[07:40:10] Found bwa - /usr/local/bin/bwa
[07:40:10] Found bcftools - /usr/local/bin/bcftools
[07:40:10] Found samtools - /usr/local/bin/samtools
[07:40:10] Found java - /usr/local/bin/java
[07:40:10] Found snpEff - /usr/local/bin/snpEff
[07:40:10] Found samclip - /usr/local/bin/samclip
[07:40:10] Found seqtk - /usr/local/bin/seqtk
[07:40:10] Found parallel - /usr/local/bin/parallel
[07:40:10] Found freebayes - /usr/local/bin/freebayes
[07:40:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:10] Found gzip - /bin/gzip
[07:40:10] Found vt - /usr/local/bin/vt
[07:40:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:40:30] This is snippy 4.6.0Show full stderr[07:40:30] This is snippy 4.6.0
[07:40:30] Written by Torsten Seemann
[07:40:30] Obtained from https://github.com/tseemann/snippy
[07:40:30] Detected operating system: linux
[07:40:30] Enabling bundled linux tools.
[07:40:30] Found bwa - /usr/local/bin/bwa
[07:40:30] Found bcftools - /usr/local/bin/bcftools
[07:40:30] Found samtools - /usr/local/bin/samtools
[07:40:30] Found java - /usr/local/bin/java
[07:40:30] Found snpEff - /usr/local/bin/snpEff
[07:40:30] Found samclip - /usr/local/bin/samclip
[07:40:30] Found seqtk - /usr/local/bin/seqtk
[07:40:30] Found parallel - /usr/local/bin/parallel
[07:40:30] Found freebayes - /usr/local/bin/freebayes
[07:40:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:30] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:30] Found gzip - /bin/gzip
[07:40:30] Found vt - /usr/local/bin/vt
[07:40:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:42:37] This is snippy 4.6.0Show full stderr[07:42:37] This is snippy 4.6.0
[07:42:37] Written by Torsten Seemann
[07:42:37] Obtained from https://github.com/tseemann/snippy
[07:42:37] Detected operating system: linux
[07:42:37] Enabling bundled linux tools.
[07:42:37] Found bwa - /usr/local/bin/bwa
[07:42:37] Found bcftools - /usr/local/bin/bcftools
[07:42:37] Found samtools - /usr/local/bin/samtools
[07:42:37] Found java - /usr/local/bin/java
[07:42:37] Found snpEff - /usr/local/bin/snpEff
[07:42:37] Found samclip - /usr/local/bin/samclip
[07:42:37] Found seqtk - /usr/local/bin/seqtk
[07:42:37] Found parallel - /usr/local/bin/parallel
[07:42:37] Found freebayes - /usr/local/bin/freebayes
[07:42:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:37] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:37] Found gzip - /bin/gzip
[07:42:37] Found vt - /usr/local/bin/vt
[07:42:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:43:01] This is snippy 4.6.0Show full stderr[07:43:01] This is snippy 4.6.0
[07:43:01] Written by Torsten Seemann
[07:43:01] Obtained from https://github.com/tseemann/snippy
[07:43:01] Detected operating system: linux
[07:43:01] Enabling bundled linux tools.
[07:43:01] Found bwa - /usr/local/bin/bwa
[07:43:01] Found bcftools - /usr/local/bin/bcftools
[07:43:01] Found samtools - /usr/local/bin/samtools
[07:43:01] Found java - /usr/local/bin/java
[07:43:01] Found snpEff - /usr/local/bin/snpEff
[07:43:01] Found samclip - /usr/local/bin/samclip
[07:43:01] Found seqtk - /usr/local/bin/seqtk
[07:43:01] Found parallel - /usr/local/bin/parallel
[07:43:01] Found freebayes - /usr/local/bin/freebayes
[07:43:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:01] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:01] Found gzip - /bin/gzip
[07:43:01] Found vt - /usr/local/bin/vt
[07:43:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:43:16] This is snippy 4.6.0Show full stderr[07:43:16] This is snippy 4.6.0
[07:43:16] Written by Torsten Seemann
[07:43:16] Obtained from https://github.com/tseemann/snippy
[07:43:16] Detected operating system: linux
[07:43:16] Enabling bundled linux tools.
[07:43:16] Found bwa - /usr/local/bin/bwa
[07:43:16] Found bcftools - /usr/local/bin/bcftools
[07:43:16] Found samtools - /usr/local/bin/samtools
[07:43:16] Found java - /usr/local/bin/java
[07:43:16] Found snpEff - /usr/local/bin/snpEff
[07:43:16] Found samclip - /usr/local/bin/samclip
[07:43:16] Found seqtk - /usr/local/bin/seqtk
[07:43:16] Found parallel - /usr/local/bin/parallel
[07:43:16] Found freebayes - /usr/local/bin/freebayes
[07:43:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:16] Found gzip - /bin/gzip
[07:43:16] Found vt - /usr/local/bin/vt
[07:43:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:43:35] This is snippy 4.6.0Show full stderr[07:43:35] This is snippy 4.6.0
[07:43:35] Written by Torsten Seemann
[07:43:35] Obtained from https://github.com/tseemann/snippy
[07:43:35] Detected operating system: linux
[07:43:35] Enabling bundled linux tools.
[07:43:35] Found bwa - /usr/local/bin/bwa
[07:43:35] Found bcftools - /usr/local/bin/bcftools
[07:43:35] Found samtools - /usr/local/bin/samtools
[07:43:35] Found java - /usr/local/bin/java
[07:43:35] Found snpEff - /usr/local/bin/snpEff
[07:43:35] Found samclip - /usr/local/bin/samclip
[07:43:35] Found seqtk - /usr/local/bin/seqtk
[07:43:35] Found parallel - /usr/local/bin/parallel
[07:43:35] Found freebayes - /usr/local/bin/freebayes
[07:43:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:35] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:35] Found gzip - /bin/gzip
[07:43:35] Found vt - /usr/local/bin/vt
[07:43:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:43:54] This is snippy 4.6.0Show full stderr[07:43:54] This is snippy 4.6.0
[07:43:54] Written by Torsten Seemann
[07:43:54] Obtained from https://github.com/tseemann/snippy
[07:43:54] Detected operating system: linux
[07:43:54] Enabling bundled linux tools.
[07:43:54] Found bwa - /usr/local/bin/bwa
[07:43:54] Found bcftools - /usr/local/bin/bcftools
[07:43:54] Found samtools - /usr/local/bin/samtools
[07:43:54] Found java - /usr/local/bin/java
[07:43:54] Found snpEff - /usr/local/bin/snpEff
[07:43:54] Found samclip - /usr/local/bin/samclip
[07:43:54] Found seqtk - /usr/local/bin/seqtk
[07:43:54] Found parallel - /usr/local/bin/parallel
[07:43:54] Found freebayes - /usr/local/bin/freebayes
[07:43:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:54] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:54] Found gzip - /bin/gzip
[07:43:54] Found vt - /usr/local/bin/vt
[07:43:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:01] This is snippy 4.6.0Show full stderr[07:45:01] This is snippy 4.6.0
[07:45:01] Written by Torsten Seemann
[07:45:01] Obtained from https://github.com/tseemann/snippy
[07:45:01] Detected operating system: linux
[07:45:01] Enabling bundled linux tools.
[07:45:01] Found bwa - /usr/local/bin/bwa
[07:45:01] Found bcftools - /usr/local/bin/bcftools
[07:45:01] Found samtools - /usr/local/bin/samtools
[07:45:01] Found java - /usr/local/bin/java
[07:45:01] Found snpEff - /usr/local/bin/snpEff
[07:45:01] Found samclip - /usr/local/bin/samclip
[07:45:01] Found seqtk - /usr/local/bin/seqtk
[07:45:01] Found parallel - /usr/local/bin/parallel
[07:45:01] Found freebayes - /usr/local/bin/freebayes
[07:45:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:01] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:01] Found gzip - /bin/gzip
[07:45:01] Found vt - /usr/local/bin/vt
[07:45:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:34] This is snippy 4.6.0Show full stderr[07:45:34] This is snippy 4.6.0
[07:45:34] Written by Torsten Seemann
[07:45:34] Obtained from https://github.com/tseemann/snippy
[07:45:34] Detected operating system: linux
[07:45:34] Enabling bundled linux tools.
[07:45:34] Found bwa - /usr/local/bin/bwa
[07:45:34] Found bcftools - /usr/local/bin/bcftools
[07:45:34] Found samtools - /usr/local/bin/samtools
[07:45:34] Found java - /usr/local/bin/java
[07:45:34] Found snpEff - /usr/local/bin/snpEff
[07:45:34] Found samclip - /usr/local/bin/samclip
[07:45:34] Found seqtk - /usr/local/bin/seqtk
[07:45:34] Found parallel - /usr/local/bin/parallel
[07:45:34] Found freebayes - /usr/local/bin/freebayes
[07:45:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:34] Found gzip - /bin/gzip
[07:45:34] Found vt - /usr/local/bin/vt
[07:45:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:46:07] This is snippy 4.6.0Show full stderr[07:46:07] This is snippy 4.6.0
[07:46:07] Written by Torsten Seemann
[07:46:07] Obtained from https://github.com/tseemann/snippy
[07:46:07] Detected operating system: linux
[07:46:07] Enabling bundled linux tools.
[07:46:07] Found bwa - /usr/local/bin/bwa
[07:46:07] Found bcftools - /usr/local/bin/bcftools
[07:46:07] Found samtools - /usr/local/bin/samtools
[07:46:07] Found java - /usr/local/bin/java
[07:46:07] Found snpEff - /usr/local/bin/snpEff
[07:46:07] Found samclip - /usr/local/bin/samclip
[07:46:07] Found seqtk - /usr/local/bin/seqtk
[07:46:07] Found parallel - /usr/local/bin/parallel
[07:46:07] Found freebayes - /usr/local/bin/freebayes
[07:46:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:07] Found gzip - /bin/gzip
[07:46:07] Found vt - /usr/local/bin/vt
[07:46:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:46:36] This is snippy 4.6.0Show full stderr[07:46:36] This is snippy 4.6.0
[07:46:36] Written by Torsten Seemann
[07:46:36] Obtained from https://github.com/tseemann/snippy
[07:46:36] Detected operating system: linux
[07:46:36] Enabling bundled linux tools.
[07:46:37] Found bwa - /usr/local/bin/bwa
[07:46:37] Found bcftools - /usr/local/bin/bcftools
[07:46:37] Found samtools - /usr/local/bin/samtools
[07:46:37] Found java - /usr/local/bin/java
[07:46:37] Found snpEff - /usr/local/bin/snpEff
[07:46:37] Found samclip - /usr/local/bin/samclip
[07:46:37] Found seqtk - /usr/local/bin/seqtk
[07:46:37] Found parallel - /usr/local/bin/parallel
[07:46:37] Found freebayes - /usr/local/bin/freebayes
[07:46:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:37] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:37] Found gzip - /bin/gzip
[07:46:37] Found vt - /usr/local/bin/vt
[07:46:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:43:28] This is snippy 4.6.0Show full stderr[07:43:28] This is snippy 4.6.0
[07:43:28] Written by Torsten Seemann
[07:43:28] Obtained from https://github.com/tseemann/snippy
[07:43:28] Detected operating system: linux
[07:43:28] Enabling bundled linux tools.
[07:43:28] Found bwa - /usr/local/bin/bwa
[07:43:28] Found bcftools - /usr/local/bin/bcftools
[07:43:28] Found samtools - /usr/local/bin/samtools
[07:43:28] Found java - /usr/local/bin/java
[07:43:28] Found snpEff - /usr/local/bin/snpEff
[07:43:28] Found samclip - /usr/local/bin/samclip
[07:43:28] Found seqtk - /usr/local/bin/seqtk
[07:43:28] Found parallel - /usr/local/bin/parallel
[07:43:28] Found freebayes - /usr/local/bin/freebayes
[07:43:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:28] Found gzip - /bin/gzip
[07:43:28] Found vt - /usr/local/bin/vt
[07:43:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:43:38] This is snippy 4.6.0Show full stderr[07:43:38] This is snippy 4.6.0
[07:43:38] Written by Torsten Seemann
[07:43:38] Obtained from https://github.com/tseemann/snippy
[07:43:38] Detected operating system: linux
[07:43:38] Enabling bundled linux tools.
[07:43:38] Found bwa - /usr/local/bin/bwa
[07:43:38] Found bcftools - /usr/local/bin/bcftools
[07:43:38] Found samtools - /usr/local/bin/samtools
[07:43:38] Found java - /usr/local/bin/java
[07:43:38] Found snpEff - /usr/local/bin/snpEff
[07:43:38] Found samclip - /usr/local/bin/samclip
[07:43:38] Found seqtk - /usr/local/bin/seqtk
[07:43:38] Found parallel - /usr/local/bin/parallel
[07:43:38] Found freebayes - /usr/local/bin/freebayes
[07:43:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:38] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:38] Found gzip - /bin/gzip
[07:43:38] Found vt - /usr/local/bin/vt
[07:43:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:43:41] This is snippy 4.6.0Show full stderr[07:43:41] This is snippy 4.6.0
[07:43:41] Written by Torsten Seemann
[07:43:41] Obtained from https://github.com/tseemann/snippy
[07:43:41] Detected operating system: linux
[07:43:41] Enabling bundled linux tools.
[07:43:41] Found bwa - /usr/local/bin/bwa
[07:43:41] Found bcftools - /usr/local/bin/bcftools
[07:43:41] Found samtools - /usr/local/bin/samtools
[07:43:41] Found java - /usr/local/bin/java
[07:43:41] Found snpEff - /usr/local/bin/snpEff
[07:43:41] Found samclip - /usr/local/bin/samclip
[07:43:41] Found seqtk - /usr/local/bin/seqtk
[07:43:41] Found parallel - /usr/local/bin/parallel
[07:43:41] Found freebayes - /usr/local/bin/freebayes
[07:43:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:41] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:41] Found gzip - /bin/gzip
[07:43:41] Found vt - /usr/local/bin/vt
[07:43:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:00] This is snippy 4.6.0Show full stderr[07:44:00] This is snippy 4.6.0
[07:44:00] Written by Torsten Seemann
[07:44:00] Obtained from https://github.com/tseemann/snippy
[07:44:00] Detected operating system: linux
[07:44:00] Enabling bundled linux tools.
[07:44:00] Found bwa - /usr/local/bin/bwa
[07:44:00] Found bcftools - /usr/local/bin/bcftools
[07:44:00] Found samtools - /usr/local/bin/samtools
[07:44:00] Found java - /usr/local/bin/java
[07:44:00] Found snpEff - /usr/local/bin/snpEff
[07:44:00] Found samclip - /usr/local/bin/samclip
[07:44:00] Found seqtk - /usr/local/bin/seqtk
[07:44:00] Found parallel - /usr/local/bin/parallel
[07:44:00] Found freebayes - /usr/local/bin/freebayes
[07:44:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:00] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:00] Found gzip - /bin/gzip
[07:44:00] Found vt - /usr/local/bin/vt
[07:44:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:35] This is snippy 4.6.0Show full stderr[07:44:35] This is snippy 4.6.0
[07:44:35] Written by Torsten Seemann
[07:44:35] Obtained from https://github.com/tseemann/snippy
[07:44:35] Detected operating system: linux
[07:44:35] Enabling bundled linux tools.
[07:44:35] Found bwa - /usr/local/bin/bwa
[07:44:35] Found bcftools - /usr/local/bin/bcftools
[07:44:35] Found samtools - /usr/local/bin/samtools
[07:44:35] Found java - /usr/local/bin/java
[07:44:35] Found snpEff - /usr/local/bin/snpEff
[07:44:35] Found samclip - /usr/local/bin/samclip
[07:44:35] Found seqtk - /usr/local/bin/seqtk
[07:44:35] Found parallel - /usr/local/bin/parallel
[07:44:35] Found freebayes - /usr/local/bin/freebayes
[07:44:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:35] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:35] Found gzip - /bin/gzip
[07:44:35] Found vt - /usr/local/bin/vt
[07:44:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:58] This is snippy 4.6.0Show full stderr[07:44:58] This is snippy 4.6.0
[07:44:58] Written by Torsten Seemann
[07:44:58] Obtained from https://github.com/tseemann/snippy
[07:44:58] Detected operating system: linux
[07:44:58] Enabling bundled linux tools.
[07:44:58] Found bwa - /usr/local/bin/bwa
[07:44:58] Found bcftools - /usr/local/bin/bcftools
[07:44:58] Found samtools - /usr/local/bin/samtools
[07:44:58] Found java - /usr/local/bin/java
[07:44:58] Found snpEff - /usr/local/bin/snpEff
[07:44:58] Found samclip - /usr/local/bin/samclip
[07:44:58] Found seqtk - /usr/local/bin/seqtk
[07:44:58] Found parallel - /usr/local/bin/parallel
[07:44:58] Found freebayes - /usr/local/bin/freebayes
[07:44:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:58] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:58] Found gzip - /bin/gzip
[07:44:58] Found vt - /usr/local/bin/vt
[07:44:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:10] This is snippy 4.6.0Show full stderr[07:45:10] This is snippy 4.6.0
[07:45:10] Written by Torsten Seemann
[07:45:10] Obtained from https://github.com/tseemann/snippy
[07:45:10] Detected operating system: linux
[07:45:10] Enabling bundled linux tools.
[07:45:10] Found bwa - /usr/local/bin/bwa
[07:45:10] Found bcftools - /usr/local/bin/bcftools
[07:45:10] Found samtools - /usr/local/bin/samtools
[07:45:10] Found java - /usr/local/bin/java
[07:45:10] Found snpEff - /usr/local/bin/snpEff
[07:45:10] Found samclip - /usr/local/bin/samclip
[07:45:10] Found seqtk - /usr/local/bin/seqtk
[07:45:10] Found parallel - /usr/local/bin/parallel
[07:45:10] Found freebayes - /usr/local/bin/freebayes
[07:45:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:10] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:10] Found gzip - /bin/gzip
[07:45:10] Found vt - /usr/local/bin/vt
[07:45:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:22] This is snippy 4.6.0Show full stderr[07:45:22] This is snippy 4.6.0
[07:45:22] Written by Torsten Seemann
[07:45:22] Obtained from https://github.com/tseemann/snippy
[07:45:22] Detected operating system: linux
[07:45:22] Enabling bundled linux tools.
[07:45:22] Found bwa - /usr/local/bin/bwa
[07:45:22] Found bcftools - /usr/local/bin/bcftools
[07:45:22] Found samtools - /usr/local/bin/samtools
[07:45:22] Found java - /usr/local/bin/java
[07:45:22] Found snpEff - /usr/local/bin/snpEff
[07:45:22] Found samclip - /usr/local/bin/samclip
[07:45:22] Found seqtk - /usr/local/bin/seqtk
[07:45:22] Found parallel - /usr/local/bin/parallel
[07:45:22] Found freebayes - /usr/local/bin/freebayes
[07:45:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:22] Found gzip - /bin/gzip
[07:45:22] Found vt - /usr/local/bin/vt
[07:45:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:46:22] This is snippy 4.6.0Show full stderr[07:46:22] This is snippy 4.6.0
[07:46:22] Written by Torsten Seemann
[07:46:22] Obtained from https://github.com/tseemann/snippy
[07:46:22] Detected operating system: linux
[07:46:22] Enabling bundled linux tools.
[07:46:22] Found bwa - /usr/local/bin/bwa
[07:46:22] Found bcftools - /usr/local/bin/bcftools
[07:46:22] Found samtools - /usr/local/bin/samtools
[07:46:22] Found java - /usr/local/bin/java
[07:46:22] Found snpEff - /usr/local/bin/snpEff
[07:46:22] Found samclip - /usr/local/bin/samclip
[07:46:22] Found seqtk - /usr/local/bin/seqtk
[07:46:22] Found parallel - /usr/local/bin/parallel
[07:46:22] Found freebayes - /usr/local/bin/freebayes
[07:46:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:22] Found gzip - /bin/gzip
[07:46:22] Found vt - /usr/local/bin/vt
[07:46:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:38:28] This is snippy 4.6.0Show full stderr[07:38:28] This is snippy 4.6.0
[07:38:28] Written by Torsten Seemann
[07:38:28] Obtained from https://github.com/tseemann/snippy
[07:38:28] Detected operating system: linux
[07:38:28] Enabling bundled linux tools.
[07:38:28] Found bwa - /usr/local/bin/bwa
[07:38:28] Found bcftools - /usr/local/bin/bcftools
[07:38:28] Found samtools - /usr/local/bin/samtools
[07:38:28] Found java - /usr/local/bin/java
[07:38:28] Found snpEff - /usr/local/bin/snpEff
[07:38:28] Found samclip - /usr/local/bin/samclip
[07:38:28] Found seqtk - /usr/local/bin/seqtk
[07:38:28] Found parallel - /usr/local/bin/parallel
[07:38:28] Found freebayes - /usr/local/bin/freebayes
[07:38:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:38:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:38:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:38:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:38:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:38:28] Found gzip - /bin/gzip
[07:38:28] Found vt - /usr/local/bin/vt
[07:38:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:38:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:38:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:38:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:38:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:38:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:38:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:38:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:40:24] This is snippy 4.6.0Show full stderr[07:40:24] This is snippy 4.6.0
[07:40:24] Written by Torsten Seemann
[07:40:24] Obtained from https://github.com/tseemann/snippy
[07:40:24] Detected operating system: linux
[07:40:24] Enabling bundled linux tools.
[07:40:24] Found bwa - /usr/local/bin/bwa
[07:40:24] Found bcftools - /usr/local/bin/bcftools
[07:40:24] Found samtools - /usr/local/bin/samtools
[07:40:24] Found java - /usr/local/bin/java
[07:40:24] Found snpEff - /usr/local/bin/snpEff
[07:40:25] Found samclip - /usr/local/bin/samclip
[07:40:25] Found seqtk - /usr/local/bin/seqtk
[07:40:25] Found parallel - /usr/local/bin/parallel
[07:40:25] Found freebayes - /usr/local/bin/freebayes
[07:40:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:25] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:25] Found gzip - /bin/gzip
[07:40:25] Found vt - /usr/local/bin/vt
[07:40:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:40:50] This is snippy 4.6.0Show full stderr[07:40:50] This is snippy 4.6.0
[07:40:50] Written by Torsten Seemann
[07:40:50] Obtained from https://github.com/tseemann/snippy
[07:40:50] Detected operating system: linux
[07:40:50] Enabling bundled linux tools.
[07:40:51] Found bwa - /usr/local/bin/bwa
[07:40:51] Found bcftools - /usr/local/bin/bcftools
[07:40:51] Found samtools - /usr/local/bin/samtools
[07:40:51] Found java - /usr/local/bin/java
[07:40:51] Found snpEff - /usr/local/bin/snpEff
[07:40:51] Found samclip - /usr/local/bin/samclip
[07:40:51] Found seqtk - /usr/local/bin/seqtk
[07:40:51] Found parallel - /usr/local/bin/parallel
[07:40:51] Found freebayes - /usr/local/bin/freebayes
[07:40:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:40:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:40:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:40:51] Found vcfuniq - /usr/local/bin/vcfuniq
[07:40:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:40:51] Found gzip - /bin/gzip
[07:40:51] Found vt - /usr/local/bin/vt
[07:40:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:40:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:40:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:40:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:40:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:40:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:40:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:40:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:41:13] This is snippy 4.6.0Show full stderr[07:41:13] This is snippy 4.6.0
[07:41:13] Written by Torsten Seemann
[07:41:13] Obtained from https://github.com/tseemann/snippy
[07:41:13] Detected operating system: linux
[07:41:13] Enabling bundled linux tools.
[07:41:13] Found bwa - /usr/local/bin/bwa
[07:41:13] Found bcftools - /usr/local/bin/bcftools
[07:41:13] Found samtools - /usr/local/bin/samtools
[07:41:13] Found java - /usr/local/bin/java
[07:41:13] Found snpEff - /usr/local/bin/snpEff
[07:41:13] Found samclip - /usr/local/bin/samclip
[07:41:13] Found seqtk - /usr/local/bin/seqtk
[07:41:13] Found parallel - /usr/local/bin/parallel
[07:41:13] Found freebayes - /usr/local/bin/freebayes
[07:41:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:41:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:41:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:41:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:41:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:41:13] Found gzip - /bin/gzip
[07:41:13] Found vt - /usr/local/bin/vt
[07:41:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:41:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:41:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:41:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:41:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:41:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:41:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:41:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:41:16] This is snippy 4.6.0Show full stderr[07:41:16] This is snippy 4.6.0
[07:41:16] Written by Torsten Seemann
[07:41:16] Obtained from https://github.com/tseemann/snippy
[07:41:16] Detected operating system: linux
[07:41:16] Enabling bundled linux tools.
[07:41:16] Found bwa - /usr/local/bin/bwa
[07:41:16] Found bcftools - /usr/local/bin/bcftools
[07:41:16] Found samtools - /usr/local/bin/samtools
[07:41:16] Found java - /usr/local/bin/java
[07:41:16] Found snpEff - /usr/local/bin/snpEff
[07:41:16] Found samclip - /usr/local/bin/samclip
[07:41:16] Found seqtk - /usr/local/bin/seqtk
[07:41:16] Found parallel - /usr/local/bin/parallel
[07:41:16] Found freebayes - /usr/local/bin/freebayes
[07:41:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:41:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:41:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:41:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:41:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:41:16] Found gzip - /bin/gzip
[07:41:16] Found vt - /usr/local/bin/vt
[07:41:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:41:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:41:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:41:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:41:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:41:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:41:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:41:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:41:40] This is snippy 4.6.0Show full stderr[07:41:40] This is snippy 4.6.0
[07:41:40] Written by Torsten Seemann
[07:41:40] Obtained from https://github.com/tseemann/snippy
[07:41:40] Detected operating system: linux
[07:41:40] Enabling bundled linux tools.
[07:41:40] Found bwa - /usr/local/bin/bwa
[07:41:40] Found bcftools - /usr/local/bin/bcftools
[07:41:40] Found samtools - /usr/local/bin/samtools
[07:41:40] Found java - /usr/local/bin/java
[07:41:40] Found snpEff - /usr/local/bin/snpEff
[07:41:40] Found samclip - /usr/local/bin/samclip
[07:41:40] Found seqtk - /usr/local/bin/seqtk
[07:41:40] Found parallel - /usr/local/bin/parallel
[07:41:40] Found freebayes - /usr/local/bin/freebayes
[07:41:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:41:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:41:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:41:40] Found vcfuniq - /usr/local/bin/vcfuniq
[07:41:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:41:40] Found gzip - /bin/gzip
[07:41:40] Found vt - /usr/local/bin/vt
[07:41:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:41:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:41:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:41:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:41:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:41:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:41:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:41:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:41:42] This is snippy 4.6.0Show full stderr[07:41:42] This is snippy 4.6.0
[07:41:42] Written by Torsten Seemann
[07:41:42] Obtained from https://github.com/tseemann/snippy
[07:41:42] Detected operating system: linux
[07:41:42] Enabling bundled linux tools.
[07:41:42] Found bwa - /usr/local/bin/bwa
[07:41:42] Found bcftools - /usr/local/bin/bcftools
[07:41:42] Found samtools - /usr/local/bin/samtools
[07:41:42] Found java - /usr/local/bin/java
[07:41:43] Found snpEff - /usr/local/bin/snpEff
[07:41:43] Found samclip - /usr/local/bin/samclip
[07:41:43] Found seqtk - /usr/local/bin/seqtk
[07:41:43] Found parallel - /usr/local/bin/parallel
[07:41:43] Found freebayes - /usr/local/bin/freebayes
[07:41:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:41:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:41:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:41:43] Found vcfuniq - /usr/local/bin/vcfuniq
[07:41:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:41:43] Found gzip - /bin/gzip
[07:41:43] Found vt - /usr/local/bin/vt
[07:41:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:41:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:41:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:41:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:41:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:41:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:41:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:41:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:47:34] This is snippy 4.6.0Show full stderr[07:47:34] This is snippy 4.6.0
[07:47:34] Written by Torsten Seemann
[07:47:34] Obtained from https://github.com/tseemann/snippy
[07:47:34] Detected operating system: linux
[07:47:34] Enabling bundled linux tools.
[07:47:34] Found bwa - /usr/local/bin/bwa
[07:47:34] Found bcftools - /usr/local/bin/bcftools
[07:47:34] Found samtools - /usr/local/bin/samtools
[07:47:34] Found java - /usr/local/bin/java
[07:47:34] Found snpEff - /usr/local/bin/snpEff
[07:47:34] Found samclip - /usr/local/bin/samclip
[07:47:34] Found seqtk - /usr/local/bin/seqtk
[07:47:34] Found parallel - /usr/local/bin/parallel
[07:47:34] Found freebayes - /usr/local/bin/freebayes
[07:47:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:47:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:47:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:47:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:47:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:47:34] Found gzip - /bin/gzip
[07:47:34] Found vt - /usr/local/bin/vt
[07:47:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:47:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:47:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:47:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:47:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:47:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:47:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:47:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:47:44] This is snippy 4.6.0Show full stderr[07:47:44] This is snippy 4.6.0
[07:47:44] Written by Torsten Seemann
[07:47:44] Obtained from https://github.com/tseemann/snippy
[07:47:44] Detected operating system: linux
[07:47:44] Enabling bundled linux tools.
[07:47:44] Found bwa - /usr/local/bin/bwa
[07:47:44] Found bcftools - /usr/local/bin/bcftools
[07:47:44] Found samtools - /usr/local/bin/samtools
[07:47:44] Found java - /usr/local/bin/java
[07:47:44] Found snpEff - /usr/local/bin/snpEff
[07:47:44] Found samclip - /usr/local/bin/samclip
[07:47:44] Found seqtk - /usr/local/bin/seqtk
[07:47:44] Found parallel - /usr/local/bin/parallel
[07:47:44] Found freebayes - /usr/local/bin/freebayes
[07:47:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:47:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:47:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:47:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:47:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:47:44] Found gzip - /bin/gzip
[07:47:44] Found vt - /usr/local/bin/vt
[07:47:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:47:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:47:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:47:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:47:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:47:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:47:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:47:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:47:47] This is snippy 4.6.0Show full stderr[07:47:47] This is snippy 4.6.0
[07:47:47] Written by Torsten Seemann
[07:47:47] Obtained from https://github.com/tseemann/snippy
[07:47:47] Detected operating system: linux
[07:47:47] Enabling bundled linux tools.
[07:47:47] Found bwa - /usr/local/bin/bwa
[07:47:47] Found bcftools - /usr/local/bin/bcftools
[07:47:47] Found samtools - /usr/local/bin/samtools
[07:47:47] Found java - /usr/local/bin/java
[07:47:47] Found snpEff - /usr/local/bin/snpEff
[07:47:47] Found samclip - /usr/local/bin/samclip
[07:47:47] Found seqtk - /usr/local/bin/seqtk
[07:47:47] Found parallel - /usr/local/bin/parallel
[07:47:47] Found freebayes - /usr/local/bin/freebayes
[07:47:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:47:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:47:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:47:47] Found vcfuniq - /usr/local/bin/vcfuniq
[07:47:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:47:47] Found gzip - /bin/gzip
[07:47:47] Found vt - /usr/local/bin/vt
[07:47:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:47:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:47:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:47:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:47:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:47:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:47:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:47:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:20] This is snippy 4.6.0Show full stderr[07:48:20] This is snippy 4.6.0
[07:48:20] Written by Torsten Seemann
[07:48:20] Obtained from https://github.com/tseemann/snippy
[07:48:20] Detected operating system: linux
[07:48:20] Enabling bundled linux tools.
[07:48:20] Found bwa - /usr/local/bin/bwa
[07:48:20] Found bcftools - /usr/local/bin/bcftools
[07:48:20] Found samtools - /usr/local/bin/samtools
[07:48:20] Found java - /usr/local/bin/java
[07:48:20] Found snpEff - /usr/local/bin/snpEff
[07:48:20] Found samclip - /usr/local/bin/samclip
[07:48:20] Found seqtk - /usr/local/bin/seqtk
[07:48:20] Found parallel - /usr/local/bin/parallel
[07:48:20] Found freebayes - /usr/local/bin/freebayes
[07:48:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:20] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:20] Found gzip - /bin/gzip
[07:48:20] Found vt - /usr/local/bin/vt
[07:48:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:23] This is snippy 4.6.0Show full stderr[07:48:23] This is snippy 4.6.0
[07:48:23] Written by Torsten Seemann
[07:48:23] Obtained from https://github.com/tseemann/snippy
[07:48:23] Detected operating system: linux
[07:48:23] Enabling bundled linux tools.
[07:48:23] Found bwa - /usr/local/bin/bwa
[07:48:23] Found bcftools - /usr/local/bin/bcftools
[07:48:23] Found samtools - /usr/local/bin/samtools
[07:48:23] Found java - /usr/local/bin/java
[07:48:23] Found snpEff - /usr/local/bin/snpEff
[07:48:23] Found samclip - /usr/local/bin/samclip
[07:48:23] Found seqtk - /usr/local/bin/seqtk
[07:48:23] Found parallel - /usr/local/bin/parallel
[07:48:23] Found freebayes - /usr/local/bin/freebayes
[07:48:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:23] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:23] Found gzip - /bin/gzip
[07:48:23] Found vt - /usr/local/bin/vt
[07:48:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:29] This is snippy 4.6.0Show full stderr[07:48:29] This is snippy 4.6.0
[07:48:29] Written by Torsten Seemann
[07:48:29] Obtained from https://github.com/tseemann/snippy
[07:48:29] Detected operating system: linux
[07:48:29] Enabling bundled linux tools.
[07:48:29] Found bwa - /usr/local/bin/bwa
[07:48:29] Found bcftools - /usr/local/bin/bcftools
[07:48:29] Found samtools - /usr/local/bin/samtools
[07:48:29] Found java - /usr/local/bin/java
[07:48:29] Found snpEff - /usr/local/bin/snpEff
[07:48:29] Found samclip - /usr/local/bin/samclip
[07:48:29] Found seqtk - /usr/local/bin/seqtk
[07:48:29] Found parallel - /usr/local/bin/parallel
[07:48:29] Found freebayes - /usr/local/bin/freebayes
[07:48:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:29] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:29] Found gzip - /bin/gzip
[07:48:29] Found vt - /usr/local/bin/vt
[07:48:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:32] This is snippy 4.6.0Show full stderr[07:48:32] This is snippy 4.6.0
[07:48:32] Written by Torsten Seemann
[07:48:32] Obtained from https://github.com/tseemann/snippy
[07:48:32] Detected operating system: linux
[07:48:32] Enabling bundled linux tools.
[07:48:32] Found bwa - /usr/local/bin/bwa
[07:48:32] Found bcftools - /usr/local/bin/bcftools
[07:48:32] Found samtools - /usr/local/bin/samtools
[07:48:32] Found java - /usr/local/bin/java
[07:48:32] Found snpEff - /usr/local/bin/snpEff
[07:48:32] Found samclip - /usr/local/bin/samclip
[07:48:32] Found seqtk - /usr/local/bin/seqtk
[07:48:32] Found parallel - /usr/local/bin/parallel
[07:48:32] Found freebayes - /usr/local/bin/freebayes
[07:48:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:32] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:32] Found gzip - /bin/gzip
[07:48:32] Found vt - /usr/local/bin/vt
[07:48:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:34] This is snippy 4.6.0Show full stderr[07:48:34] This is snippy 4.6.0
[07:48:34] Written by Torsten Seemann
[07:48:34] Obtained from https://github.com/tseemann/snippy
[07:48:34] Detected operating system: linux
[07:48:34] Enabling bundled linux tools.
[07:48:34] Found bwa - /usr/local/bin/bwa
[07:48:34] Found bcftools - /usr/local/bin/bcftools
[07:48:34] Found samtools - /usr/local/bin/samtools
[07:48:34] Found java - /usr/local/bin/java
[07:48:34] Found snpEff - /usr/local/bin/snpEff
[07:48:34] Found samclip - /usr/local/bin/samclip
[07:48:34] Found seqtk - /usr/local/bin/seqtk
[07:48:34] Found parallel - /usr/local/bin/parallel
[07:48:34] Found freebayes - /usr/local/bin/freebayes
[07:48:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:34] Found gzip - /bin/gzip
[07:48:34] Found vt - /usr/local/bin/vt
[07:48:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:38] This is snippy 4.6.0Show full stderr[07:48:38] This is snippy 4.6.0
[07:48:38] Written by Torsten Seemann
[07:48:38] Obtained from https://github.com/tseemann/snippy
[07:48:38] Detected operating system: linux
[07:48:38] Enabling bundled linux tools.
[07:48:38] Found bwa - /usr/local/bin/bwa
[07:48:38] Found bcftools - /usr/local/bin/bcftools
[07:48:38] Found samtools - /usr/local/bin/samtools
[07:48:38] Found java - /usr/local/bin/java
[07:48:38] Found snpEff - /usr/local/bin/snpEff
[07:48:38] Found samclip - /usr/local/bin/samclip
[07:48:38] Found seqtk - /usr/local/bin/seqtk
[07:48:38] Found parallel - /usr/local/bin/parallel
[07:48:38] Found freebayes - /usr/local/bin/freebayes
[07:48:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:38] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:38] Found gzip - /bin/gzip
[07:48:38] Found vt - /usr/local/bin/vt
[07:48:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:44] This is snippy 4.6.0Show full stderr[07:48:44] This is snippy 4.6.0
[07:48:44] Written by Torsten Seemann
[07:48:44] Obtained from https://github.com/tseemann/snippy
[07:48:44] Detected operating system: linux
[07:48:44] Enabling bundled linux tools.
[07:48:44] Found bwa - /usr/local/bin/bwa
[07:48:44] Found bcftools - /usr/local/bin/bcftools
[07:48:44] Found samtools - /usr/local/bin/samtools
[07:48:44] Found java - /usr/local/bin/java
[07:48:44] Found snpEff - /usr/local/bin/snpEff
[07:48:44] Found samclip - /usr/local/bin/samclip
[07:48:44] Found seqtk - /usr/local/bin/seqtk
[07:48:44] Found parallel - /usr/local/bin/parallel
[07:48:44] Found freebayes - /usr/local/bin/freebayes
[07:48:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:44] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:44] Found gzip - /bin/gzip
[07:48:44] Found vt - /usr/local/bin/vt
[07:48:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:42:07] This is snippy 4.6.0Show full stderr[07:42:07] This is snippy 4.6.0
[07:42:07] Written by Torsten Seemann
[07:42:07] Obtained from https://github.com/tseemann/snippy
[07:42:07] Detected operating system: linux
[07:42:07] Enabling bundled linux tools.
[07:42:07] Found bwa - /usr/local/bin/bwa
[07:42:07] Found bcftools - /usr/local/bin/bcftools
[07:42:07] Found samtools - /usr/local/bin/samtools
[07:42:07] Found java - /usr/local/bin/java
[07:42:07] Found snpEff - /usr/local/bin/snpEff
[07:42:07] Found samclip - /usr/local/bin/samclip
[07:42:07] Found seqtk - /usr/local/bin/seqtk
[07:42:07] Found parallel - /usr/local/bin/parallel
[07:42:07] Found freebayes - /usr/local/bin/freebayes
[07:42:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:07] Found gzip - /bin/gzip
[07:42:07] Found vt - /usr/local/bin/vt
[07:42:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:42:25] This is snippy 4.6.0Show full stderr[07:42:25] This is snippy 4.6.0
[07:42:25] Written by Torsten Seemann
[07:42:25] Obtained from https://github.com/tseemann/snippy
[07:42:25] Detected operating system: linux
[07:42:25] Enabling bundled linux tools.
[07:42:25] Found bwa - /usr/local/bin/bwa
[07:42:25] Found bcftools - /usr/local/bin/bcftools
[07:42:25] Found samtools - /usr/local/bin/samtools
[07:42:25] Found java - /usr/local/bin/java
[07:42:25] Found snpEff - /usr/local/bin/snpEff
[07:42:25] Found samclip - /usr/local/bin/samclip
[07:42:25] Found seqtk - /usr/local/bin/seqtk
[07:42:25] Found parallel - /usr/local/bin/parallel
[07:42:25] Found freebayes - /usr/local/bin/freebayes
[07:42:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:25] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:25] Found gzip - /bin/gzip
[07:42:25] Found vt - /usr/local/bin/vt
[07:42:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:42:46] This is snippy 4.6.0Show full stderr[07:42:46] This is snippy 4.6.0
[07:42:46] Written by Torsten Seemann
[07:42:46] Obtained from https://github.com/tseemann/snippy
[07:42:46] Detected operating system: linux
[07:42:46] Enabling bundled linux tools.
[07:42:46] Found bwa - /usr/local/bin/bwa
[07:42:46] Found bcftools - /usr/local/bin/bcftools
[07:42:46] Found samtools - /usr/local/bin/samtools
[07:42:46] Found java - /usr/local/bin/java
[07:42:46] Found snpEff - /usr/local/bin/snpEff
[07:42:46] Found samclip - /usr/local/bin/samclip
[07:42:46] Found seqtk - /usr/local/bin/seqtk
[07:42:46] Found parallel - /usr/local/bin/parallel
[07:42:46] Found freebayes - /usr/local/bin/freebayes
[07:42:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:46] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:46] Found gzip - /bin/gzip
[07:42:46] Found vt - /usr/local/bin/vt
[07:42:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:43:07] This is snippy 4.6.0Show full stderr[07:43:07] This is snippy 4.6.0
[07:43:07] Written by Torsten Seemann
[07:43:07] Obtained from https://github.com/tseemann/snippy
[07:43:07] Detected operating system: linux
[07:43:07] Enabling bundled linux tools.
[07:43:07] Found bwa - /usr/local/bin/bwa
[07:43:07] Found bcftools - /usr/local/bin/bcftools
[07:43:07] Found samtools - /usr/local/bin/samtools
[07:43:07] Found java - /usr/local/bin/java
[07:43:07] Found snpEff - /usr/local/bin/snpEff
[07:43:07] Found samclip - /usr/local/bin/samclip
[07:43:07] Found seqtk - /usr/local/bin/seqtk
[07:43:07] Found parallel - /usr/local/bin/parallel
[07:43:07] Found freebayes - /usr/local/bin/freebayes
[07:43:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:07] Found gzip - /bin/gzip
[07:43:07] Found vt - /usr/local/bin/vt
[07:43:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:22] This is snippy 4.6.0Show full stderr[07:44:22] This is snippy 4.6.0
[07:44:22] Written by Torsten Seemann
[07:44:22] Obtained from https://github.com/tseemann/snippy
[07:44:22] Detected operating system: linux
[07:44:22] Enabling bundled linux tools.
[07:44:22] Found bwa - /usr/local/bin/bwa
[07:44:22] Found bcftools - /usr/local/bin/bcftools
[07:44:22] Found samtools - /usr/local/bin/samtools
[07:44:22] Found java - /usr/local/bin/java
[07:44:22] Found snpEff - /usr/local/bin/snpEff
[07:44:22] Found samclip - /usr/local/bin/samclip
[07:44:22] Found seqtk - /usr/local/bin/seqtk
[07:44:22] Found parallel - /usr/local/bin/parallel
[07:44:22] Found freebayes - /usr/local/bin/freebayes
[07:44:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:22] Found gzip - /bin/gzip
[07:44:22] Found vt - /usr/local/bin/vt
[07:44:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:46] This is snippy 4.6.0Show full stderr[07:44:46] This is snippy 4.6.0
[07:44:46] Written by Torsten Seemann
[07:44:46] Obtained from https://github.com/tseemann/snippy
[07:44:46] Detected operating system: linux
[07:44:46] Enabling bundled linux tools.
[07:44:46] Found bwa - /usr/local/bin/bwa
[07:44:46] Found bcftools - /usr/local/bin/bcftools
[07:44:46] Found samtools - /usr/local/bin/samtools
[07:44:46] Found java - /usr/local/bin/java
[07:44:46] Found snpEff - /usr/local/bin/snpEff
[07:44:46] Found samclip - /usr/local/bin/samclip
[07:44:46] Found seqtk - /usr/local/bin/seqtk
[07:44:46] Found parallel - /usr/local/bin/parallel
[07:44:46] Found freebayes - /usr/local/bin/freebayes
[07:44:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:46] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:46] Found gzip - /bin/gzip
[07:44:46] Found vt - /usr/local/bin/vt
[07:44:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:49] This is snippy 4.6.0Show full stderr[07:44:49] This is snippy 4.6.0
[07:44:49] Written by Torsten Seemann
[07:44:49] Obtained from https://github.com/tseemann/snippy
[07:44:49] Detected operating system: linux
[07:44:49] Enabling bundled linux tools.
[07:44:49] Found bwa - /usr/local/bin/bwa
[07:44:49] Found bcftools - /usr/local/bin/bcftools
[07:44:49] Found samtools - /usr/local/bin/samtools
[07:44:49] Found java - /usr/local/bin/java
[07:44:49] Found snpEff - /usr/local/bin/snpEff
[07:44:49] Found samclip - /usr/local/bin/samclip
[07:44:49] Found seqtk - /usr/local/bin/seqtk
[07:44:49] Found parallel - /usr/local/bin/parallel
[07:44:49] Found freebayes - /usr/local/bin/freebayes
[07:44:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:49] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:49] Found gzip - /bin/gzip
[07:44:49] Found vt - /usr/local/bin/vt
[07:44:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:55] This is snippy 4.6.0Show full stderr[07:44:55] This is snippy 4.6.0
[07:44:55] Written by Torsten Seemann
[07:44:55] Obtained from https://github.com/tseemann/snippy
[07:44:55] Detected operating system: linux
[07:44:55] Enabling bundled linux tools.
[07:44:55] Found bwa - /usr/local/bin/bwa
[07:44:55] Found bcftools - /usr/local/bin/bcftools
[07:44:55] Found samtools - /usr/local/bin/samtools
[07:44:55] Found java - /usr/local/bin/java
[07:44:55] Found snpEff - /usr/local/bin/snpEff
[07:44:55] Found samclip - /usr/local/bin/samclip
[07:44:55] Found seqtk - /usr/local/bin/seqtk
[07:44:55] Found parallel - /usr/local/bin/parallel
[07:44:55] Found freebayes - /usr/local/bin/freebayes
[07:44:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:55] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:55] Found gzip - /bin/gzip
[07:44:55] Found vt - /usr/local/bin/vt
[07:44:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:04] This is snippy 4.6.0Show full stderr[07:45:04] This is snippy 4.6.0
[07:45:04] Written by Torsten Seemann
[07:45:04] Obtained from https://github.com/tseemann/snippy
[07:45:04] Detected operating system: linux
[07:45:04] Enabling bundled linux tools.
[07:45:04] Found bwa - /usr/local/bin/bwa
[07:45:04] Found bcftools - /usr/local/bin/bcftools
[07:45:04] Found samtools - /usr/local/bin/samtools
[07:45:04] Found java - /usr/local/bin/java
[07:45:04] Found snpEff - /usr/local/bin/snpEff
[07:45:04] Found samclip - /usr/local/bin/samclip
[07:45:04] Found seqtk - /usr/local/bin/seqtk
[07:45:04] Found parallel - /usr/local/bin/parallel
[07:45:04] Found freebayes - /usr/local/bin/freebayes
[07:45:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:04] Found gzip - /bin/gzip
[07:45:04] Found vt - /usr/local/bin/vt
[07:45:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:16] This is snippy 4.6.0Show full stderr[07:45:16] This is snippy 4.6.0
[07:45:16] Written by Torsten Seemann
[07:45:16] Obtained from https://github.com/tseemann/snippy
[07:45:16] Detected operating system: linux
[07:45:16] Enabling bundled linux tools.
[07:45:16] Found bwa - /usr/local/bin/bwa
[07:45:16] Found bcftools - /usr/local/bin/bcftools
[07:45:16] Found samtools - /usr/local/bin/samtools
[07:45:16] Found java - /usr/local/bin/java
[07:45:16] Found snpEff - /usr/local/bin/snpEff
[07:45:16] Found samclip - /usr/local/bin/samclip
[07:45:16] Found seqtk - /usr/local/bin/seqtk
[07:45:16] Found parallel - /usr/local/bin/parallel
[07:45:16] Found freebayes - /usr/local/bin/freebayes
[07:45:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:16] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:16] Found gzip - /bin/gzip
[07:45:16] Found vt - /usr/local/bin/vt
[07:45:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:47:04] This is snippy 4.6.0Show full stderr[07:47:04] This is snippy 4.6.0
[07:47:04] Written by Torsten Seemann
[07:47:04] Obtained from https://github.com/tseemann/snippy
[07:47:04] Detected operating system: linux
[07:47:04] Enabling bundled linux tools.
[07:47:04] Found bwa - /usr/local/bin/bwa
[07:47:04] Found bcftools - /usr/local/bin/bcftools
[07:47:04] Found samtools - /usr/local/bin/samtools
[07:47:04] Found java - /usr/local/bin/java
[07:47:04] Found snpEff - /usr/local/bin/snpEff
[07:47:04] Found samclip - /usr/local/bin/samclip
[07:47:04] Found seqtk - /usr/local/bin/seqtk
[07:47:04] Found parallel - /usr/local/bin/parallel
[07:47:04] Found freebayes - /usr/local/bin/freebayes
[07:47:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:47:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:47:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:47:04] Found vcfuniq - /usr/local/bin/vcfuniq
[07:47:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:47:04] Found gzip - /bin/gzip
[07:47:04] Found vt - /usr/local/bin/vt
[07:47:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:47:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:47:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:47:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:47:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:47:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:47:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:47:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:47:19] This is snippy 4.6.0Show full stderr[07:47:19] This is snippy 4.6.0
[07:47:19] Written by Torsten Seemann
[07:47:19] Obtained from https://github.com/tseemann/snippy
[07:47:19] Detected operating system: linux
[07:47:19] Enabling bundled linux tools.
[07:47:19] Found bwa - /usr/local/bin/bwa
[07:47:19] Found bcftools - /usr/local/bin/bcftools
[07:47:19] Found samtools - /usr/local/bin/samtools
[07:47:19] Found java - /usr/local/bin/java
[07:47:19] Found snpEff - /usr/local/bin/snpEff
[07:47:19] Found samclip - /usr/local/bin/samclip
[07:47:19] Found seqtk - /usr/local/bin/seqtk
[07:47:19] Found parallel - /usr/local/bin/parallel
[07:47:19] Found freebayes - /usr/local/bin/freebayes
[07:47:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:47:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:47:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:47:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:47:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:47:19] Found gzip - /bin/gzip
[07:47:19] Found vt - /usr/local/bin/vt
[07:47:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:47:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:47:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:47:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:47:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:47:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:47:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:47:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:47:59] This is snippy 4.6.0Show full stderr[07:47:59] This is snippy 4.6.0
[07:47:59] Written by Torsten Seemann
[07:47:59] Obtained from https://github.com/tseemann/snippy
[07:47:59] Detected operating system: linux
[07:47:59] Enabling bundled linux tools.
[07:47:59] Found bwa - /usr/local/bin/bwa
[07:47:59] Found bcftools - /usr/local/bin/bcftools
[07:47:59] Found samtools - /usr/local/bin/samtools
[07:47:59] Found java - /usr/local/bin/java
[07:47:59] Found snpEff - /usr/local/bin/snpEff
[07:47:59] Found samclip - /usr/local/bin/samclip
[07:47:59] Found seqtk - /usr/local/bin/seqtk
[07:47:59] Found parallel - /usr/local/bin/parallel
[07:47:59] Found freebayes - /usr/local/bin/freebayes
[07:47:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:47:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:47:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:47:59] Found vcfuniq - /usr/local/bin/vcfuniq
[07:47:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:47:59] Found gzip - /bin/gzip
[07:47:59] Found vt - /usr/local/bin/vt
[07:47:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:47:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:47:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:47:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:47:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:02] This is snippy 4.6.0Show full stderr[07:48:02] This is snippy 4.6.0
[07:48:02] Written by Torsten Seemann
[07:48:02] Obtained from https://github.com/tseemann/snippy
[07:48:02] Detected operating system: linux
[07:48:02] Enabling bundled linux tools.
[07:48:02] Found bwa - /usr/local/bin/bwa
[07:48:02] Found bcftools - /usr/local/bin/bcftools
[07:48:02] Found samtools - /usr/local/bin/samtools
[07:48:02] Found java - /usr/local/bin/java
[07:48:02] Found snpEff - /usr/local/bin/snpEff
[07:48:02] Found samclip - /usr/local/bin/samclip
[07:48:02] Found seqtk - /usr/local/bin/seqtk
[07:48:02] Found parallel - /usr/local/bin/parallel
[07:48:02] Found freebayes - /usr/local/bin/freebayes
[07:48:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:02] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:02] Found gzip - /bin/gzip
[07:48:02] Found vt - /usr/local/bin/vt
[07:48:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:14] This is snippy 4.6.0Show full stderr[07:48:14] This is snippy 4.6.0
[07:48:14] Written by Torsten Seemann
[07:48:14] Obtained from https://github.com/tseemann/snippy
[07:48:14] Detected operating system: linux
[07:48:14] Enabling bundled linux tools.
[07:48:14] Found bwa - /usr/local/bin/bwa
[07:48:14] Found bcftools - /usr/local/bin/bcftools
[07:48:14] Found samtools - /usr/local/bin/samtools
[07:48:14] Found java - /usr/local/bin/java
[07:48:14] Found snpEff - /usr/local/bin/snpEff
[07:48:14] Found samclip - /usr/local/bin/samclip
[07:48:14] Found seqtk - /usr/local/bin/seqtk
[07:48:14] Found parallel - /usr/local/bin/parallel
[07:48:14] Found freebayes - /usr/local/bin/freebayes
[07:48:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:14] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:14] Found gzip - /bin/gzip
[07:48:14] Found vt - /usr/local/bin/vt
[07:48:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:17] This is snippy 4.6.0Show full stderr[07:48:17] This is snippy 4.6.0
[07:48:17] Written by Torsten Seemann
[07:48:17] Obtained from https://github.com/tseemann/snippy
[07:48:17] Detected operating system: linux
[07:48:17] Enabling bundled linux tools.
[07:48:17] Found bwa - /usr/local/bin/bwa
[07:48:17] Found bcftools - /usr/local/bin/bcftools
[07:48:17] Found samtools - /usr/local/bin/samtools
[07:48:17] Found java - /usr/local/bin/java
[07:48:17] Found snpEff - /usr/local/bin/snpEff
[07:48:17] Found samclip - /usr/local/bin/samclip
[07:48:17] Found seqtk - /usr/local/bin/seqtk
[07:48:17] Found parallel - /usr/local/bin/parallel
[07:48:17] Found freebayes - /usr/local/bin/freebayes
[07:48:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:17] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:17] Found gzip - /bin/gzip
[07:48:17] Found vt - /usr/local/bin/vt
[07:48:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:42:52] This is snippy 4.6.0Show full stderr[07:42:52] This is snippy 4.6.0
[07:42:52] Written by Torsten Seemann
[07:42:52] Obtained from https://github.com/tseemann/snippy
[07:42:52] Detected operating system: linux
[07:42:52] Enabling bundled linux tools.
[07:42:52] Found bwa - /usr/local/bin/bwa
[07:42:52] Found bcftools - /usr/local/bin/bcftools
[07:42:52] Found samtools - /usr/local/bin/samtools
[07:42:52] Found java - /usr/local/bin/java
[07:42:52] Found snpEff - /usr/local/bin/snpEff
[07:42:52] Found samclip - /usr/local/bin/samclip
[07:42:52] Found seqtk - /usr/local/bin/seqtk
[07:42:52] Found parallel - /usr/local/bin/parallel
[07:42:52] Found freebayes - /usr/local/bin/freebayes
[07:42:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:52] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:52] Found gzip - /bin/gzip
[07:42:52] Found vt - /usr/local/bin/vt
[07:42:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:43:34] This is snippy 4.6.0Show full stderr[07:43:34] This is snippy 4.6.0
[07:43:34] Written by Torsten Seemann
[07:43:34] Obtained from https://github.com/tseemann/snippy
[07:43:34] Detected operating system: linux
[07:43:34] Enabling bundled linux tools.
[07:43:34] Found bwa - /usr/local/bin/bwa
[07:43:34] Found bcftools - /usr/local/bin/bcftools
[07:43:34] Found samtools - /usr/local/bin/samtools
[07:43:34] Found java - /usr/local/bin/java
[07:43:34] Found snpEff - /usr/local/bin/snpEff
[07:43:34] Found samclip - /usr/local/bin/samclip
[07:43:34] Found seqtk - /usr/local/bin/seqtk
[07:43:34] Found parallel - /usr/local/bin/parallel
[07:43:34] Found freebayes - /usr/local/bin/freebayes
[07:43:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:34] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:34] Found gzip - /bin/gzip
[07:43:34] Found vt - /usr/local/bin/vt
[07:43:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:43:51] This is snippy 4.6.0Show full stderr[07:43:51] This is snippy 4.6.0
[07:43:51] Written by Torsten Seemann
[07:43:51] Obtained from https://github.com/tseemann/snippy
[07:43:51] Detected operating system: linux
[07:43:51] Enabling bundled linux tools.
[07:43:51] Found bwa - /usr/local/bin/bwa
[07:43:51] Found bcftools - /usr/local/bin/bcftools
[07:43:51] Found samtools - /usr/local/bin/samtools
[07:43:51] Found java - /usr/local/bin/java
[07:43:51] Found snpEff - /usr/local/bin/snpEff
[07:43:51] Found samclip - /usr/local/bin/samclip
[07:43:51] Found seqtk - /usr/local/bin/seqtk
[07:43:51] Found parallel - /usr/local/bin/parallel
[07:43:51] Found freebayes - /usr/local/bin/freebayes
[07:43:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:43:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:43:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:43:51] Found vcfuniq - /usr/local/bin/vcfuniq
[07:43:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:43:51] Found gzip - /bin/gzip
[07:43:51] Found vt - /usr/local/bin/vt
[07:43:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:43:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:43:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:43:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:43:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:43:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:43:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:43:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:07] This is snippy 4.6.0Show full stderr[07:44:07] This is snippy 4.6.0
[07:44:07] Written by Torsten Seemann
[07:44:07] Obtained from https://github.com/tseemann/snippy
[07:44:07] Detected operating system: linux
[07:44:07] Enabling bundled linux tools.
[07:44:07] Found bwa - /usr/local/bin/bwa
[07:44:07] Found bcftools - /usr/local/bin/bcftools
[07:44:07] Found samtools - /usr/local/bin/samtools
[07:44:07] Found java - /usr/local/bin/java
[07:44:07] Found snpEff - /usr/local/bin/snpEff
[07:44:07] Found samclip - /usr/local/bin/samclip
[07:44:07] Found seqtk - /usr/local/bin/seqtk
[07:44:07] Found parallel - /usr/local/bin/parallel
[07:44:07] Found freebayes - /usr/local/bin/freebayes
[07:44:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:07] Found gzip - /bin/gzip
[07:44:07] Found vt - /usr/local/bin/vt
[07:44:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:31] This is snippy 4.6.0Show full stderr[07:44:31] This is snippy 4.6.0
[07:44:31] Written by Torsten Seemann
[07:44:31] Obtained from https://github.com/tseemann/snippy
[07:44:31] Detected operating system: linux
[07:44:31] Enabling bundled linux tools.
[07:44:31] Found bwa - /usr/local/bin/bwa
[07:44:31] Found bcftools - /usr/local/bin/bcftools
[07:44:31] Found samtools - /usr/local/bin/samtools
[07:44:31] Found java - /usr/local/bin/java
[07:44:31] Found snpEff - /usr/local/bin/snpEff
[07:44:31] Found samclip - /usr/local/bin/samclip
[07:44:31] Found seqtk - /usr/local/bin/seqtk
[07:44:31] Found parallel - /usr/local/bin/parallel
[07:44:31] Found freebayes - /usr/local/bin/freebayes
[07:44:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:31] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:31] Found gzip - /bin/gzip
[07:44:31] Found vt - /usr/local/bin/vt
[07:44:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:53] This is snippy 4.6.0Show full stderr[07:48:53] This is snippy 4.6.0
[07:48:53] Written by Torsten Seemann
[07:48:53] Obtained from https://github.com/tseemann/snippy
[07:48:53] Detected operating system: linux
[07:48:53] Enabling bundled linux tools.
[07:48:53] Found bwa - /usr/local/bin/bwa
[07:48:53] Found bcftools - /usr/local/bin/bcftools
[07:48:53] Found samtools - /usr/local/bin/samtools
[07:48:53] Found java - /usr/local/bin/java
[07:48:53] Found snpEff - /usr/local/bin/snpEff
[07:48:53] Found samclip - /usr/local/bin/samclip
[07:48:53] Found seqtk - /usr/local/bin/seqtk
[07:48:53] Found parallel - /usr/local/bin/parallel
[07:48:53] Found freebayes - /usr/local/bin/freebayes
[07:48:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:53] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:53] Found gzip - /bin/gzip
[07:48:53] Found vt - /usr/local/bin/vt
[07:48:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:48:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:48:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:48:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:48:59] This is snippy 4.6.0Show full stderr[07:48:59] This is snippy 4.6.0
[07:48:59] Written by Torsten Seemann
[07:48:59] Obtained from https://github.com/tseemann/snippy
[07:48:59] Detected operating system: linux
[07:48:59] Enabling bundled linux tools.
[07:48:59] Found bwa - /usr/local/bin/bwa
[07:48:59] Found bcftools - /usr/local/bin/bcftools
[07:48:59] Found samtools - /usr/local/bin/samtools
[07:48:59] Found java - /usr/local/bin/java
[07:48:59] Found snpEff - /usr/local/bin/snpEff
[07:48:59] Found samclip - /usr/local/bin/samclip
[07:48:59] Found seqtk - /usr/local/bin/seqtk
[07:48:59] Found parallel - /usr/local/bin/parallel
[07:48:59] Found freebayes - /usr/local/bin/freebayes
[07:48:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:48:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:48:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:48:59] Found vcfuniq - /usr/local/bin/vcfuniq
[07:48:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:48:59] Found gzip - /bin/gzip
[07:48:59] Found vt - /usr/local/bin/vt
[07:48:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:48:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:48:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:48:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:48:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:49:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:49:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:49:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:49:07] This is snippy 4.6.0Show full stderr[07:49:07] This is snippy 4.6.0
[07:49:07] Written by Torsten Seemann
[07:49:07] Obtained from https://github.com/tseemann/snippy
[07:49:07] Detected operating system: linux
[07:49:07] Enabling bundled linux tools.
[07:49:07] Found bwa - /usr/local/bin/bwa
[07:49:07] Found bcftools - /usr/local/bin/bcftools
[07:49:07] Found samtools - /usr/local/bin/samtools
[07:49:07] Found java - /usr/local/bin/java
[07:49:07] Found snpEff - /usr/local/bin/snpEff
[07:49:07] Found samclip - /usr/local/bin/samclip
[07:49:07] Found seqtk - /usr/local/bin/seqtk
[07:49:07] Found parallel - /usr/local/bin/parallel
[07:49:07] Found freebayes - /usr/local/bin/freebayes
[07:49:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:49:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:49:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:49:07] Found vcfuniq - /usr/local/bin/vcfuniq
[07:49:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:49:07] Found gzip - /bin/gzip
[07:49:07] Found vt - /usr/local/bin/vt
[07:49:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:49:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:49:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:49:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:49:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:49:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:49:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:49:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:49:13] This is snippy 4.6.0Show full stderr[07:49:13] This is snippy 4.6.0
[07:49:13] Written by Torsten Seemann
[07:49:13] Obtained from https://github.com/tseemann/snippy
[07:49:13] Detected operating system: linux
[07:49:13] Enabling bundled linux tools.
[07:49:13] Found bwa - /usr/local/bin/bwa
[07:49:13] Found bcftools - /usr/local/bin/bcftools
[07:49:13] Found samtools - /usr/local/bin/samtools
[07:49:13] Found java - /usr/local/bin/java
[07:49:13] Found snpEff - /usr/local/bin/snpEff
[07:49:13] Found samclip - /usr/local/bin/samclip
[07:49:13] Found seqtk - /usr/local/bin/seqtk
[07:49:13] Found parallel - /usr/local/bin/parallel
[07:49:13] Found freebayes - /usr/local/bin/freebayes
[07:49:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:49:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:49:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:49:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:49:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:49:13] Found gzip - /bin/gzip
[07:49:13] Found vt - /usr/local/bin/vt
[07:49:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:49:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:49:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:49:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:49:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:49:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:49:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:49:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:49:22] This is snippy 4.6.0Show full stderr[07:49:22] This is snippy 4.6.0
[07:49:22] Written by Torsten Seemann
[07:49:22] Obtained from https://github.com/tseemann/snippy
[07:49:22] Detected operating system: linux
[07:49:22] Enabling bundled linux tools.
[07:49:22] Found bwa - /usr/local/bin/bwa
[07:49:22] Found bcftools - /usr/local/bin/bcftools
[07:49:22] Found samtools - /usr/local/bin/samtools
[07:49:22] Found java - /usr/local/bin/java
[07:49:22] Found snpEff - /usr/local/bin/snpEff
[07:49:22] Found samclip - /usr/local/bin/samclip
[07:49:22] Found seqtk - /usr/local/bin/seqtk
[07:49:22] Found parallel - /usr/local/bin/parallel
[07:49:22] Found freebayes - /usr/local/bin/freebayes
[07:49:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:49:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:49:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:49:22] Found vcfuniq - /usr/local/bin/vcfuniq
[07:49:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:49:22] Found gzip - /bin/gzip
[07:49:22] Found vt - /usr/local/bin/vt
[07:49:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:49:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:49:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:49:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:49:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:49:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:49:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:49:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:49:28] This is snippy 4.6.0Show full stderr[07:49:28] This is snippy 4.6.0
[07:49:28] Written by Torsten Seemann
[07:49:28] Obtained from https://github.com/tseemann/snippy
[07:49:28] Detected operating system: linux
[07:49:28] Enabling bundled linux tools.
[07:49:28] Found bwa - /usr/local/bin/bwa
[07:49:28] Found bcftools - /usr/local/bin/bcftools
[07:49:28] Found samtools - /usr/local/bin/samtools
[07:49:28] Found java - /usr/local/bin/java
[07:49:28] Found snpEff - /usr/local/bin/snpEff
[07:49:28] Found samclip - /usr/local/bin/samclip
[07:49:28] Found seqtk - /usr/local/bin/seqtk
[07:49:28] Found parallel - /usr/local/bin/parallel
[07:49:28] Found freebayes - /usr/local/bin/freebayes
[07:49:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:49:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:49:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:49:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:49:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:49:28] Found gzip - /bin/gzip
[07:49:28] Found vt - /usr/local/bin/vt
[07:49:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:49:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:49:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:49:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:49:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:49:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:49:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:49:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:49:37] This is snippy 4.6.0Show full stderr[07:49:37] This is snippy 4.6.0
[07:49:37] Written by Torsten Seemann
[07:49:37] Obtained from https://github.com/tseemann/snippy
[07:49:37] Detected operating system: linux
[07:49:37] Enabling bundled linux tools.
[07:49:37] Found bwa - /usr/local/bin/bwa
[07:49:37] Found bcftools - /usr/local/bin/bcftools
[07:49:37] Found samtools - /usr/local/bin/samtools
[07:49:37] Found java - /usr/local/bin/java
[07:49:37] Found snpEff - /usr/local/bin/snpEff
[07:49:37] Found samclip - /usr/local/bin/samclip
[07:49:37] Found seqtk - /usr/local/bin/seqtk
[07:49:37] Found parallel - /usr/local/bin/parallel
[07:49:37] Found freebayes - /usr/local/bin/freebayes
[07:49:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:49:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:49:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:49:37] Found vcfuniq - /usr/local/bin/vcfuniq
[07:49:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:49:37] Found gzip - /bin/gzip
[07:49:37] Found vt - /usr/local/bin/vt
[07:49:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:49:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:49:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:49:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:49:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:49:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:49:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:49:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:49:40] This is snippy 4.6.0Show full stderr[07:49:40] This is snippy 4.6.0
[07:49:40] Written by Torsten Seemann
[07:49:40] Obtained from https://github.com/tseemann/snippy
[07:49:40] Detected operating system: linux
[07:49:40] Enabling bundled linux tools.
[07:49:40] Found bwa - /usr/local/bin/bwa
[07:49:40] Found bcftools - /usr/local/bin/bcftools
[07:49:40] Found samtools - /usr/local/bin/samtools
[07:49:40] Found java - /usr/local/bin/java
[07:49:40] Found snpEff - /usr/local/bin/snpEff
[07:49:40] Found samclip - /usr/local/bin/samclip
[07:49:40] Found seqtk - /usr/local/bin/seqtk
[07:49:40] Found parallel - /usr/local/bin/parallel
[07:49:40] Found freebayes - /usr/local/bin/freebayes
[07:49:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:49:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:49:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:49:40] Found vcfuniq - /usr/local/bin/vcfuniq
[07:49:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:49:40] Found gzip - /bin/gzip
[07:49:40] Found vt - /usr/local/bin/vt
[07:49:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:49:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:49:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:49:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:49:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:49:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:49:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:49:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:49:49] This is snippy 4.6.0Show full stderr[07:49:49] This is snippy 4.6.0
[07:49:49] Written by Torsten Seemann
[07:49:49] Obtained from https://github.com/tseemann/snippy
[07:49:49] Detected operating system: linux
[07:49:49] Enabling bundled linux tools.
[07:49:49] Found bwa - /usr/local/bin/bwa
[07:49:49] Found bcftools - /usr/local/bin/bcftools
[07:49:49] Found samtools - /usr/local/bin/samtools
[07:49:49] Found java - /usr/local/bin/java
[07:49:49] Found snpEff - /usr/local/bin/snpEff
[07:49:49] Found samclip - /usr/local/bin/samclip
[07:49:49] Found seqtk - /usr/local/bin/seqtk
[07:49:49] Found parallel - /usr/local/bin/parallel
[07:49:49] Found freebayes - /usr/local/bin/freebayes
[07:49:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:49:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:49:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:49:49] Found vcfuniq - /usr/local/bin/vcfuniq
[07:49:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:49:49] Found gzip - /bin/gzip
[07:49:49] Found vt - /usr/local/bin/vt
[07:49:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:49:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:49:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:49:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:49:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:49:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:49:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:49:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:19] This is snippy 4.6.0Show full stderr[07:45:19] This is snippy 4.6.0
[07:45:19] Written by Torsten Seemann
[07:45:19] Obtained from https://github.com/tseemann/snippy
[07:45:19] Detected operating system: linux
[07:45:19] Enabling bundled linux tools.
[07:45:19] Found bwa - /usr/local/bin/bwa
[07:45:19] Found bcftools - /usr/local/bin/bcftools
[07:45:19] Found samtools - /usr/local/bin/samtools
[07:45:19] Found java - /usr/local/bin/java
[07:45:19] Found snpEff - /usr/local/bin/snpEff
[07:45:19] Found samclip - /usr/local/bin/samclip
[07:45:19] Found seqtk - /usr/local/bin/seqtk
[07:45:19] Found parallel - /usr/local/bin/parallel
[07:45:19] Found freebayes - /usr/local/bin/freebayes
[07:45:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:19] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:19] Found gzip - /bin/gzip
[07:45:19] Found vt - /usr/local/bin/vt
[07:45:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:28] This is snippy 4.6.0Show full stderr[07:45:28] This is snippy 4.6.0
[07:45:28] Written by Torsten Seemann
[07:45:28] Obtained from https://github.com/tseemann/snippy
[07:45:28] Detected operating system: linux
[07:45:28] Enabling bundled linux tools.
[07:45:28] Found bwa - /usr/local/bin/bwa
[07:45:28] Found bcftools - /usr/local/bin/bcftools
[07:45:28] Found samtools - /usr/local/bin/samtools
[07:45:28] Found java - /usr/local/bin/java
[07:45:28] Found snpEff - /usr/local/bin/snpEff
[07:45:28] Found samclip - /usr/local/bin/samclip
[07:45:28] Found seqtk - /usr/local/bin/seqtk
[07:45:28] Found parallel - /usr/local/bin/parallel
[07:45:28] Found freebayes - /usr/local/bin/freebayes
[07:45:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:28] Found gzip - /bin/gzip
[07:45:28] Found vt - /usr/local/bin/vt
[07:45:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:37] This is snippy 4.6.0Show full stderr[07:45:37] This is snippy 4.6.0
[07:45:37] Written by Torsten Seemann
[07:45:37] Obtained from https://github.com/tseemann/snippy
[07:45:37] Detected operating system: linux
[07:45:37] Enabling bundled linux tools.
[07:45:37] Found bwa - /usr/local/bin/bwa
[07:45:37] Found bcftools - /usr/local/bin/bcftools
[07:45:37] Found samtools - /usr/local/bin/samtools
[07:45:37] Found java - /usr/local/bin/java
[07:45:37] Found snpEff - /usr/local/bin/snpEff
[07:45:37] Found samclip - /usr/local/bin/samclip
[07:45:37] Found seqtk - /usr/local/bin/seqtk
[07:45:37] Found parallel - /usr/local/bin/parallel
[07:45:37] Found freebayes - /usr/local/bin/freebayes
[07:45:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:37] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:37] Found gzip - /bin/gzip
[07:45:37] Found vt - /usr/local/bin/vt
[07:45:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:43] This is snippy 4.6.0Show full stderr[07:45:43] This is snippy 4.6.0
[07:45:43] Written by Torsten Seemann
[07:45:43] Obtained from https://github.com/tseemann/snippy
[07:45:43] Detected operating system: linux
[07:45:43] Enabling bundled linux tools.
[07:45:43] Found bwa - /usr/local/bin/bwa
[07:45:43] Found bcftools - /usr/local/bin/bcftools
[07:45:43] Found samtools - /usr/local/bin/samtools
[07:45:43] Found java - /usr/local/bin/java
[07:45:43] Found snpEff - /usr/local/bin/snpEff
[07:45:43] Found samclip - /usr/local/bin/samclip
[07:45:43] Found seqtk - /usr/local/bin/seqtk
[07:45:43] Found parallel - /usr/local/bin/parallel
[07:45:43] Found freebayes - /usr/local/bin/freebayes
[07:45:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:43] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:43] Found gzip - /bin/gzip
[07:45:43] Found vt - /usr/local/bin/vt
[07:45:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:46] This is snippy 4.6.0Show full stderr[07:45:46] This is snippy 4.6.0
[07:45:46] Written by Torsten Seemann
[07:45:46] Obtained from https://github.com/tseemann/snippy
[07:45:46] Detected operating system: linux
[07:45:46] Enabling bundled linux tools.
[07:45:46] Found bwa - /usr/local/bin/bwa
[07:45:46] Found bcftools - /usr/local/bin/bcftools
[07:45:46] Found samtools - /usr/local/bin/samtools
[07:45:46] Found java - /usr/local/bin/java
[07:45:46] Found snpEff - /usr/local/bin/snpEff
[07:45:46] Found samclip - /usr/local/bin/samclip
[07:45:46] Found seqtk - /usr/local/bin/seqtk
[07:45:46] Found parallel - /usr/local/bin/parallel
[07:45:46] Found freebayes - /usr/local/bin/freebayes
[07:45:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:46] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:46] Found gzip - /bin/gzip
[07:45:46] Found vt - /usr/local/bin/vt
[07:45:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:49] This is snippy 4.6.0Show full stderr[07:45:49] This is snippy 4.6.0
[07:45:49] Written by Torsten Seemann
[07:45:49] Obtained from https://github.com/tseemann/snippy
[07:45:49] Detected operating system: linux
[07:45:49] Enabling bundled linux tools.
[07:45:49] Found bwa - /usr/local/bin/bwa
[07:45:49] Found bcftools - /usr/local/bin/bcftools
[07:45:49] Found samtools - /usr/local/bin/samtools
[07:45:49] Found java - /usr/local/bin/java
[07:45:49] Found snpEff - /usr/local/bin/snpEff
[07:45:49] Found samclip - /usr/local/bin/samclip
[07:45:49] Found seqtk - /usr/local/bin/seqtk
[07:45:49] Found parallel - /usr/local/bin/parallel
[07:45:49] Found freebayes - /usr/local/bin/freebayes
[07:45:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:49] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:49] Found gzip - /bin/gzip
[07:45:49] Found vt - /usr/local/bin/vt
[07:45:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:52] This is snippy 4.6.0Show full stderr[07:45:52] This is snippy 4.6.0
[07:45:52] Written by Torsten Seemann
[07:45:52] Obtained from https://github.com/tseemann/snippy
[07:45:52] Detected operating system: linux
[07:45:52] Enabling bundled linux tools.
[07:45:52] Found bwa - /usr/local/bin/bwa
[07:45:52] Found bcftools - /usr/local/bin/bcftools
[07:45:52] Found samtools - /usr/local/bin/samtools
[07:45:52] Found java - /usr/local/bin/java
[07:45:52] Found snpEff - /usr/local/bin/snpEff
[07:45:52] Found samclip - /usr/local/bin/samclip
[07:45:52] Found seqtk - /usr/local/bin/seqtk
[07:45:52] Found parallel - /usr/local/bin/parallel
[07:45:52] Found freebayes - /usr/local/bin/freebayes
[07:45:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:52] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:52] Found gzip - /bin/gzip
[07:45:52] Found vt - /usr/local/bin/vt
[07:45:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:45:58] This is snippy 4.6.0Show full stderr[07:45:58] This is snippy 4.6.0
[07:45:58] Written by Torsten Seemann
[07:45:58] Obtained from https://github.com/tseemann/snippy
[07:45:58] Detected operating system: linux
[07:45:58] Enabling bundled linux tools.
[07:45:58] Found bwa - /usr/local/bin/bwa
[07:45:58] Found bcftools - /usr/local/bin/bcftools
[07:45:58] Found samtools - /usr/local/bin/samtools
[07:45:58] Found java - /usr/local/bin/java
[07:45:58] Found snpEff - /usr/local/bin/snpEff
[07:45:58] Found samclip - /usr/local/bin/samclip
[07:45:58] Found seqtk - /usr/local/bin/seqtk
[07:45:58] Found parallel - /usr/local/bin/parallel
[07:45:58] Found freebayes - /usr/local/bin/freebayes
[07:45:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:45:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:45:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:45:58] Found vcfuniq - /usr/local/bin/vcfuniq
[07:45:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:45:58] Found gzip - /bin/gzip
[07:45:58] Found vt - /usr/local/bin/vt
[07:45:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:45:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:45:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:45:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:45:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:45:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:45:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:45:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:46:13] This is snippy 4.6.0Show full stderr[07:46:13] This is snippy 4.6.0
[07:46:13] Written by Torsten Seemann
[07:46:13] Obtained from https://github.com/tseemann/snippy
[07:46:13] Detected operating system: linux
[07:46:13] Enabling bundled linux tools.
[07:46:13] Found bwa - /usr/local/bin/bwa
[07:46:13] Found bcftools - /usr/local/bin/bcftools
[07:46:13] Found samtools - /usr/local/bin/samtools
[07:46:13] Found java - /usr/local/bin/java
[07:46:13] Found snpEff - /usr/local/bin/snpEff
[07:46:13] Found samclip - /usr/local/bin/samclip
[07:46:13] Found seqtk - /usr/local/bin/seqtk
[07:46:13] Found parallel - /usr/local/bin/parallel
[07:46:13] Found freebayes - /usr/local/bin/freebayes
[07:46:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:13] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:13] Found gzip - /bin/gzip
[07:46:13] Found vt - /usr/local/bin/vt
[07:46:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:46:28] This is snippy 4.6.0Show full stderr[07:46:28] This is snippy 4.6.0
[07:46:28] Written by Torsten Seemann
[07:46:28] Obtained from https://github.com/tseemann/snippy
[07:46:28] Detected operating system: linux
[07:46:28] Enabling bundled linux tools.
[07:46:28] Found bwa - /usr/local/bin/bwa
[07:46:28] Found bcftools - /usr/local/bin/bcftools
[07:46:28] Found samtools - /usr/local/bin/samtools
[07:46:28] Found java - /usr/local/bin/java
[07:46:28] Found snpEff - /usr/local/bin/snpEff
[07:46:28] Found samclip - /usr/local/bin/samclip
[07:46:28] Found seqtk - /usr/local/bin/seqtk
[07:46:28] Found parallel - /usr/local/bin/parallel
[07:46:28] Found freebayes - /usr/local/bin/freebayes
[07:46:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:28] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:28] Found gzip - /bin/gzip
[07:46:28] Found vt - /usr/local/bin/vt
[07:46:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:46:46] This is snippy 4.6.0Show full stderr[07:46:46] This is snippy 4.6.0
[07:46:46] Written by Torsten Seemann
[07:46:46] Obtained from https://github.com/tseemann/snippy
[07:46:46] Detected operating system: linux
[07:46:46] Enabling bundled linux tools.
[07:46:46] Found bwa - /usr/local/bin/bwa
[07:46:46] Found bcftools - /usr/local/bin/bcftools
[07:46:46] Found samtools - /usr/local/bin/samtools
[07:46:46] Found java - /usr/local/bin/java
[07:46:46] Found snpEff - /usr/local/bin/snpEff
[07:46:46] Found samclip - /usr/local/bin/samclip
[07:46:46] Found seqtk - /usr/local/bin/seqtk
[07:46:46] Found parallel - /usr/local/bin/parallel
[07:46:46] Found freebayes - /usr/local/bin/freebayes
[07:46:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:46] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:46] Found gzip - /bin/gzip
[07:46:46] Found vt - /usr/local/bin/vt
[07:46:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:46:49] This is snippy 4.6.0Show full stderr[07:46:49] This is snippy 4.6.0
[07:46:49] Written by Torsten Seemann
[07:46:49] Obtained from https://github.com/tseemann/snippy
[07:46:49] Detected operating system: linux
[07:46:49] Enabling bundled linux tools.
[07:46:49] Found bwa - /usr/local/bin/bwa
[07:46:49] Found bcftools - /usr/local/bin/bcftools
[07:46:49] Found samtools - /usr/local/bin/samtools
[07:46:49] Found java - /usr/local/bin/java
[07:46:49] Found snpEff - /usr/local/bin/snpEff
[07:46:49] Found samclip - /usr/local/bin/samclip
[07:46:49] Found seqtk - /usr/local/bin/seqtk
[07:46:49] Found parallel - /usr/local/bin/parallel
[07:46:49] Found freebayes - /usr/local/bin/freebayes
[07:46:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:46:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:46:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:46:49] Found vcfuniq - /usr/local/bin/vcfuniq
[07:46:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:46:49] Found gzip - /bin/gzip
[07:46:49] Found vt - /usr/local/bin/vt
[07:46:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:46:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:46:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:46:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:46:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:46:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:46:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:46:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:47:01] This is snippy 4.6.0Show full stderr[07:47:01] This is snippy 4.6.0
[07:47:01] Written by Torsten Seemann
[07:47:01] Obtained from https://github.com/tseemann/snippy
[07:47:01] Detected operating system: linux
[07:47:01] Enabling bundled linux tools.
[07:47:01] Found bwa - /usr/local/bin/bwa
[07:47:01] Found bcftools - /usr/local/bin/bcftools
[07:47:01] Found samtools - /usr/local/bin/samtools
[07:47:01] Found java - /usr/local/bin/java
[07:47:01] Found snpEff - /usr/local/bin/snpEff
[07:47:01] Found samclip - /usr/local/bin/samclip
[07:47:01] Found seqtk - /usr/local/bin/seqtk
[07:47:01] Found parallel - /usr/local/bin/parallel
[07:47:01] Found freebayes - /usr/local/bin/freebayes
[07:47:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:47:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:47:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:47:01] Found vcfuniq - /usr/local/bin/vcfuniq
[07:47:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:47:01] Found gzip - /bin/gzip
[07:47:01] Found vt - /usr/local/bin/vt
[07:47:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:47:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:47:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:47:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:47:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:47:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:47:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:47:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:22:28] This is snippy 4.6.0Show full stderr[08:22:28] This is snippy 4.6.0
[08:22:28] Written by Torsten Seemann
[08:22:28] Obtained from https://github.com/tseemann/snippy
[08:22:28] Detected operating system: linux
[08:22:28] Enabling bundled linux tools.
[08:22:28] Found bwa - /usr/local/bin/bwa
[08:22:28] Found bcftools - /usr/local/bin/bcftools
[08:22:28] Found samtools - /usr/local/bin/samtools
[08:22:28] Found java - /usr/local/bin/java
[08:22:28] Found snpEff - /usr/local/bin/snpEff
[08:22:28] Found samclip - /usr/local/bin/samclip
[08:22:28] Found seqtk - /usr/local/bin/seqtk
[08:22:28] Found parallel - /usr/local/bin/parallel
[08:22:28] Found freebayes - /usr/local/bin/freebayes
[08:22:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:22:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:22:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:22:28] Found vcfuniq - /usr/local/bin/vcfuniq
[08:22:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:22:28] Found gzip - /bin/gzip
[08:22:28] Found vt - /usr/local/bin/vt
[08:22:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:22:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:22:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:22:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:22:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:22:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:22:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:22:29] Using reference: /corral4/main/objects/b/2/e/dataset_b2e63dfb-6861-4d9c-a497-0b231c9ac46a.dat
[08:22:29] Treating reference as 'fasta' format.
[08:22:29] Will use 1 CPU cores.
[08:22:29] Using read file: /corral4/main/objects/4/7/b/dataset_47b089a5-7ccc-49f2-b505-f2adb97b524c.dat
[08:22:29] Creating folder: Resistance_93_fasta
[08:22:29] Changing working directory: Resistance_93_fasta
[08:22:29] Creating reference folder: reference
[08:22:29] Extracting FASTA and GFF from reference.
[08:22:29] Wrote 1 sequences to ref.fa
[08:22:29] Wrote 0 features to ref.gff
[08:22:29] Shredding /corral4/main/objects/4/7/b/dataset_47b089a5-7ccc-49f2-b505-f2adb97b524c.dat into pseudo-reads
[08:22:33] Wrote 422488 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[08:22:33] Freebayes will process 1 chunks of 3047 bp, 1 chunks at a time.
[08:22:33] Using BAM RG (Read Group) ID: Resistance_93_fasta
[08:22:33] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:22:33] Running: bwa index reference/ref.fa 2>> snps.log
[08:22:33] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[08:22:33] Running: ln -sf reference/ref.fa . 2>> snps.log
[08:22:33] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[08:22:33] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[08:22:33] Running: bwa mem -Y -M -R '@RG\tID:Resistance_93_fasta\tSM:Resistance_93_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/264/72264696/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/264/72264696/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/264/72264696/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences in reference/ref.fa.fai
[M::process] |
| 1 | [09:20:22] This is snippy 4.6.0Show full stderr[09:20:22] This is snippy 4.6.0
[09:20:22] Written by Torsten Seemann
[09:20:22] Obtained from https://github.com/tseemann/snippy
[09:20:22] Detected operating system: linux
[09:20:22] Enabling bundled linux tools.
[09:20:22] Found bwa - /usr/local/bin/bwa
[09:20:22] Found bcftools - /usr/local/bin/bcftools
[09:20:22] Found samtools - /usr/local/bin/samtools
[09:20:22] Found java - /usr/local/bin/java
[09:20:22] Found snpEff - /usr/local/bin/snpEff
[09:20:22] Found samclip - /usr/local/bin/samclip
[09:20:22] Found seqtk - /usr/local/bin/seqtk
[09:20:22] Found parallel - /usr/local/bin/parallel
[09:20:22] Found freebayes - /usr/local/bin/freebayes
[09:20:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:20:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:20:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:20:22] Found vcfuniq - /usr/local/bin/vcfuniq
[09:20:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:20:22] Found gzip - /bin/gzip
[09:20:22] Found vt - /usr/local/bin/vt
[09:20:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:20:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:20:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:20:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:20:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:20:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:20:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:20:22] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:20:23] Treating reference as 'fasta' format.
[09:20:23] Will use 1 CPU cores.
[09:20:23] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:20:23] Using read file: /corral4/main/objects/b/3/d/dataset_b3d4e3f0-7686-4f07-83e7-d370bd805280.dat
[09:20:23] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:20:23] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:20:23] Creating reference folder: reference
[09:20:23] Extracting FASTA and GFF from reference.
[09:20:31] Wrote 702 sequences to ref.fa
[09:20:31] Wrote 0 features to ref.gff
[09:20:31] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time.
[09:20:31] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:20:31] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:20:32] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 1 | [09:30:00] This is snippy 4.6.0Show full stderr[09:30:00] This is snippy 4.6.0
[09:30:00] Written by Torsten Seemann
[09:30:00] Obtained from https://github.com/tseemann/snippy
[09:30:00] Detected operating system: linux
[09:30:00] Enabling bundled linux tools.
[09:30:00] Found bwa - /usr/local/bin/bwa
[09:30:00] Found bcftools - /usr/local/bin/bcftools
[09:30:00] Found samtools - /usr/local/bin/samtools
[09:30:00] Found java - /usr/local/bin/java
[09:30:00] Found snpEff - /usr/local/bin/snpEff
[09:30:00] Found samclip - /usr/local/bin/samclip
[09:30:00] Found seqtk - /usr/local/bin/seqtk
[09:30:00] Found parallel - /usr/local/bin/parallel
[09:30:00] Found freebayes - /usr/local/bin/freebayes
[09:30:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:30:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:30:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:30:00] Found vcfuniq - /usr/local/bin/vcfuniq
[09:30:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:30:00] Found gzip - /bin/gzip
[09:30:00] Found vt - /usr/local/bin/vt
[09:30:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:30:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:30:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:30:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:30:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:30:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:30:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:30:01] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:30:02] Treating reference as 'fasta' format.
[09:30:02] Will use 1 CPU cores.
[09:30:02] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:30:02] Using read file: /corral4/main/objects/3/b/f/dataset_3bffcdc3-34b5-4333-9ca1-70773ed0ae26.dat
[09:30:02] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:30:02] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:30:02] Creating reference folder: reference
[09:30:02] Extracting FASTA and GFF from reference.
[09:30:10] Wrote 702 sequences to ref.fa
[09:30:10] Wrote 0 features to ref.gff
[09:30:10] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[09:30:10] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:30:10] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:30:10] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 1 | [09:21:44] This is snippy 4.6.0Show full stderr[09:21:44] This is snippy 4.6.0
[09:21:44] Written by Torsten Seemann
[09:21:44] Obtained from https://github.com/tseemann/snippy
[09:21:44] Detected operating system: linux
[09:21:44] Enabling bundled linux tools.
[09:21:44] Found bwa - /usr/local/bin/bwa
[09:21:44] Found bcftools - /usr/local/bin/bcftools
[09:21:44] Found samtools - /usr/local/bin/samtools
[09:21:44] Found java - /usr/local/bin/java
[09:21:44] Found snpEff - /usr/local/bin/snpEff
[09:21:44] Found samclip - /usr/local/bin/samclip
[09:21:44] Found seqtk - /usr/local/bin/seqtk
[09:21:44] Found parallel - /usr/local/bin/parallel
[09:21:44] Found freebayes - /usr/local/bin/freebayes
[09:21:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:21:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:21:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:21:44] Found vcfuniq - /usr/local/bin/vcfuniq
[09:21:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:21:44] Found gzip - /bin/gzip
[09:21:44] Found vt - /usr/local/bin/vt
[09:21:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:21:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:21:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:21:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:21:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:21:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:21:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:21:44] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:21:45] Treating reference as 'fasta' format.
[09:21:45] Will use 1 CPU cores.
[09:21:45] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:21:45] Using read file: /corral4/main/objects/6/b/1/dataset_6b1ad49a-4a2a-498d-8117-7497e94c0a80.dat
[09:21:45] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:45] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:45] Creating reference folder: reference
[09:21:45] Extracting FASTA and GFF from reference.
[09:21:53] Wrote 702 sequences to ref.fa
[09:21:53] Wrote 0 features to ref.gff
[09:21:53] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[09:21:53] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:53] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:21:53] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 1 | [09:22:01] This is snippy 4.6.0Show full stderr[09:22:01] This is snippy 4.6.0
[09:22:01] Written by Torsten Seemann
[09:22:01] Obtained from https://github.com/tseemann/snippy
[09:22:01] Detected operating system: linux
[09:22:01] Enabling bundled linux tools.
[09:22:01] Found bwa - /usr/local/bin/bwa
[09:22:01] Found bcftools - /usr/local/bin/bcftools
[09:22:01] Found samtools - /usr/local/bin/samtools
[09:22:01] Found java - /usr/local/bin/java
[09:22:01] Found snpEff - /usr/local/bin/snpEff
[09:22:01] Found samclip - /usr/local/bin/samclip
[09:22:01] Found seqtk - /usr/local/bin/seqtk
[09:22:01] Found parallel - /usr/local/bin/parallel
[09:22:01] Found freebayes - /usr/local/bin/freebayes
[09:22:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:22:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:22:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:22:01] Found vcfuniq - /usr/local/bin/vcfuniq
[09:22:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:22:01] Found gzip - /bin/gzip
[09:22:01] Found vt - /usr/local/bin/vt
[09:22:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:22:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:22:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:22:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:22:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:22:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:22:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:22:01] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:22:02] Treating reference as 'fasta' format.
[09:22:02] Will use 1 CPU cores.
[09:22:02] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:22:02] Using read file: /corral4/main/objects/e/3/8/dataset_e38132f1-37f3-4ab3-a022-cf955afaeefe.dat
[09:22:02] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:22:02] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:22:02] Creating reference folder: reference
[09:22:02] Extracting FASTA and GFF from reference.
[09:22:09] Wrote 702 sequences to ref.fa
[09:22:09] Wrote 0 features to ref.gff
[09:22:09] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time.
[09:22:09] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:22:09] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:22:10] Running: bwa index reference/ref.fa 2>> snps.log
[09:25:17] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 1 | [09:22:07] This is snippy 4.6.0Show full stderr[09:22:07] This is snippy 4.6.0
[09:22:07] Written by Torsten Seemann
[09:22:07] Obtained from https://github.com/tseemann/snippy
[09:22:07] Detected operating system: linux
[09:22:07] Enabling bundled linux tools.
[09:22:07] Found bwa - /usr/local/bin/bwa
[09:22:07] Found bcftools - /usr/local/bin/bcftools
[09:22:07] Found samtools - /usr/local/bin/samtools
[09:22:07] Found java - /usr/local/bin/java
[09:22:07] Found snpEff - /usr/local/bin/snpEff
[09:22:07] Found samclip - /usr/local/bin/samclip
[09:22:07] Found seqtk - /usr/local/bin/seqtk
[09:22:07] Found parallel - /usr/local/bin/parallel
[09:22:07] Found freebayes - /usr/local/bin/freebayes
[09:22:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:22:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:22:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:22:07] Found vcfuniq - /usr/local/bin/vcfuniq
[09:22:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:22:07] Found gzip - /bin/gzip
[09:22:07] Found vt - /usr/local/bin/vt
[09:22:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:22:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:22:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:22:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:22:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:22:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:22:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:22:08] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:22:08] Treating reference as 'fasta' format.
[09:22:08] Will use 1 CPU cores.
[09:22:08] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:22:08] Using read file: /corral4/main/objects/e/3/0/dataset_e3005d69-11fb-4397-84d6-fdd8617a4c65.dat
[09:22:08] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:22:08] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:22:08] Creating reference folder: reference
[09:22:08] Extracting FASTA and GFF from reference.
[09:22:16] Wrote 702 sequences to ref.fa
[09:22:16] Wrote 0 features to ref.gff
[09:22:16] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time.
[09:22:16] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:22:16] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:22:17] Running: bwa index reference/ref.fa 2>> snps.log
[09:25:28] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 1 | [09:25:32] This is snippy 4.6.0Show full stderr[09:25:32] This is snippy 4.6.0
[09:25:32] Written by Torsten Seemann
[09:25:32] Obtained from https://github.com/tseemann/snippy
[09:25:32] Detected operating system: linux
[09:25:32] Enabling bundled linux tools.
[09:25:32] Found bwa - /usr/local/bin/bwa
[09:25:32] Found bcftools - /usr/local/bin/bcftools
[09:25:32] Found samtools - /usr/local/bin/samtools
[09:25:32] Found java - /usr/local/bin/java
[09:25:32] Found snpEff - /usr/local/bin/snpEff
[09:25:32] Found samclip - /usr/local/bin/samclip
[09:25:32] Found seqtk - /usr/local/bin/seqtk
[09:25:32] Found parallel - /usr/local/bin/parallel
[09:25:32] Found freebayes - /usr/local/bin/freebayes
[09:25:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:25:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:25:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:25:33] Found vcfuniq - /usr/local/bin/vcfuniq
[09:25:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:25:33] Found gzip - /bin/gzip
[09:25:33] Found vt - /usr/local/bin/vt
[09:25:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:25:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:25:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:25:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:25:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:25:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:25:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:25:33] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:25:34] Treating reference as 'fasta' format.
[09:25:34] Will use 1 CPU cores.
[09:25:34] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:25:34] Using read file: /corral4/main/objects/7/f/4/dataset_7f4fdad8-5c88-45d2-be21-9de2a47232a3.dat
[09:25:34] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:25:34] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:25:34] Creating reference folder: reference
[09:25:34] Extracting FASTA and GFF from reference.
[09:25:41] Wrote 702 sequences to ref.fa
[09:25:41] Wrote 0 features to ref.gff
[09:25:42] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time.
[09:25:42] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:25:42] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:25:43] Running: bwa index reference/ref.fa 2>> snps.log
[09:28:52] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 1 | [09:25:43] This is snippy 4.6.0Show full stderr[09:25:43] This is snippy 4.6.0
[09:25:43] Written by Torsten Seemann
[09:25:43] Obtained from https://github.com/tseemann/snippy
[09:25:43] Detected operating system: linux
[09:25:43] Enabling bundled linux tools.
[09:25:43] Found bwa - /usr/local/bin/bwa
[09:25:43] Found bcftools - /usr/local/bin/bcftools
[09:25:43] Found samtools - /usr/local/bin/samtools
[09:25:43] Found java - /usr/local/bin/java
[09:25:43] Found snpEff - /usr/local/bin/snpEff
[09:25:43] Found samclip - /usr/local/bin/samclip
[09:25:43] Found seqtk - /usr/local/bin/seqtk
[09:25:43] Found parallel - /usr/local/bin/parallel
[09:25:43] Found freebayes - /usr/local/bin/freebayes
[09:25:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:25:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:25:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:25:43] Found vcfuniq - /usr/local/bin/vcfuniq
[09:25:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:25:43] Found gzip - /bin/gzip
[09:25:43] Found vt - /usr/local/bin/vt
[09:25:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:25:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:25:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:25:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:25:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:25:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:25:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:25:44] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:25:44] Treating reference as 'fasta' format.
[09:25:44] Will use 1 CPU cores.
[09:25:44] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:25:44] Using read file: /corral4/main/objects/4/f/a/dataset_4faba0fc-8fba-4a16-8711-0dcecfb7bd3a.dat
[09:25:44] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:25:44] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:25:44] Creating reference folder: reference
[09:25:44] Extracting FASTA and GFF from reference.
[09:25:52] Wrote 702 sequences to ref.fa
[09:25:52] Wrote 0 features to ref.gff
[09:25:52] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time.
[09:25:52] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:25:52] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:25:52] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 1 | [09:21:38] This is snippy 4.6.0Show full stderr[09:21:38] This is snippy 4.6.0
[09:21:38] Written by Torsten Seemann
[09:21:38] Obtained from https://github.com/tseemann/snippy
[09:21:38] Detected operating system: linux
[09:21:38] Enabling bundled linux tools.
[09:21:38] Found bwa - /usr/local/bin/bwa
[09:21:38] Found bcftools - /usr/local/bin/bcftools
[09:21:38] Found samtools - /usr/local/bin/samtools
[09:21:38] Found java - /usr/local/bin/java
[09:21:38] Found snpEff - /usr/local/bin/snpEff
[09:21:38] Found samclip - /usr/local/bin/samclip
[09:21:38] Found seqtk - /usr/local/bin/seqtk
[09:21:38] Found parallel - /usr/local/bin/parallel
[09:21:38] Found freebayes - /usr/local/bin/freebayes
[09:21:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:21:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:21:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:21:38] Found vcfuniq - /usr/local/bin/vcfuniq
[09:21:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:21:38] Found gzip - /bin/gzip
[09:21:38] Found vt - /usr/local/bin/vt
[09:21:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:21:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:21:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:21:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:21:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:21:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:21:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:21:38] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa
[09:21:39] Treating reference as 'fasta' format.
[09:21:39] Will use 1 CPU cores.
[09:21:39] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat
[09:21:39] Using read file: /corral4/main/objects/2/4/f/dataset_24f9e80a-5c47-4236-865c-7d075421adfd.dat
[09:21:39] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:39] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:39] Creating reference folder: reference
[09:21:39] Extracting FASTA and GFF from reference.
[09:21:46] Wrote 702 sequences to ref.fa
[09:21:46] Wrote 0 features to ref.gff
[09:21:47] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[09:21:47] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna
[09:21:47] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:21:47] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log |
| 1 | [13:07:15] This is snippy 4.6.0Show full stderr[13:07:15] This is snippy 4.6.0
[13:07:15] Written by Torsten Seemann
[13:07:15] Obtained from https://github.com/tseemann/snippy
[13:07:15] Detected operating system: linux
[13:07:15] Enabling bundled linux tools.
[13:07:15] Found bwa - /usr/local/bin/bwa
[13:07:15] Found bcftools - /usr/local/bin/bcftools
[13:07:15] Found samtools - /usr/local/bin/samtools
[13:07:15] Found java - /usr/local/bin/java
[13:07:15] Found snpEff - /usr/local/bin/snpEff
[13:07:15] Found samclip - /usr/local/bin/samclip
[13:07:15] Found seqtk - /usr/local/bin/seqtk
[13:07:15] Found parallel - /usr/local/bin/parallel
[13:07:15] Found freebayes - /usr/local/bin/freebayes
[13:07:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:07:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:07:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:07:15] Found vcfuniq - /usr/local/bin/vcfuniq
[13:07:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:07:15] Found gzip - /bin/gzip
[13:07:15] Found vt - /usr/local/bin/vt
[13:07:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:07:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:07:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:07:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:07:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:07:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:07:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:07:15] Using reference: /jetstream2/scratch/main/jobs/72274628/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat
[13:07:15] Treating reference as 'fasta' format.
[13:07:15] Will use 1 CPU cores.
[13:07:15] Using read file: /jetstream2/scratch/main/jobs/72274628/inputs/dataset_528cab5d-bce5-4533-80c7-807895d7ede6.dat
[13:07:15] Creating folder: Select_on_dataset_10
[13:07:15] Changing working directory: Select_on_dataset_10
[13:07:15] Creating reference folder: reference
[13:07:15] Extracting FASTA and GFF from reference.
[13:07:16] Wrote 3 sequences to ref.fa
[13:07:16] Wrote 0 features to ref.gff
[13:07:16] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[13:07:16] Using BAM RG (Read Group) ID: Select_on_dataset_10
[13:07:16] Running: samtools faidx reference/ref.fa 2>> snps.log
[13:07:16] Running: bwa index reference/ref.fa 2>> snps.log
[13:07:19] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[13:07:19] Running: ln -sf reference/ref.fa . 2>> snps.log
[13:07:19] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[13:07:19] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[13:07:19] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_10\tSM:Select_on_dataset_10' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72274628/inputs/dataset_528cab5d-bce5-4533-80c7-807895d7ede6.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72274628/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72274628/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72274628/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::process] read 1 sequences (10262635 bp)...
[M::mem_process_seqs] Processed |
| 1 | [13:17:39] This is snippy 4.6.0Show full stderr[13:17:39] This is snippy 4.6.0
[13:17:39] Written by Torsten Seemann
[13:17:39] Obtained from https://github.com/tseemann/snippy
[13:17:39] Detected operating system: linux
[13:17:39] Enabling bundled linux tools.
[13:17:39] Found bwa - /usr/local/bin/bwa
[13:17:39] Found bcftools - /usr/local/bin/bcftools
[13:17:39] Found samtools - /usr/local/bin/samtools
[13:17:39] Found java - /usr/local/bin/java
[13:17:39] Found snpEff - /usr/local/bin/snpEff
[13:17:39] Found samclip - /usr/local/bin/samclip
[13:17:39] Found seqtk - /usr/local/bin/seqtk
[13:17:39] Found parallel - /usr/local/bin/parallel
[13:17:39] Found freebayes - /usr/local/bin/freebayes
[13:17:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:17:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:17:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:17:39] Found vcfuniq - /usr/local/bin/vcfuniq
[13:17:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:17:39] Found gzip - /bin/gzip
[13:17:39] Found vt - /usr/local/bin/vt
[13:17:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:17:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:17:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:17:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:17:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:17:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:17:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:17:39] Using reference: /jetstream2/scratch/main/jobs/72274648/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat
[13:17:39] Treating reference as 'fasta' format.
[13:17:39] Will use 1 CPU cores.
[13:17:39] Using read file: /jetstream2/scratch/main/jobs/72274648/inputs/dataset_2fc7b817-f05e-4fd8-bc46-5fee29524df4.dat
[13:17:39] Creating folder: Select_on_dataset_1
[13:17:39] Changing working directory: Select_on_dataset_1
[13:17:39] Creating reference folder: reference
[13:17:39] Extracting FASTA and GFF from reference.
[13:17:40] Wrote 3 sequences to ref.fa
[13:17:40] Wrote 0 features to ref.gff
[13:17:40] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[13:17:40] Using BAM RG (Read Group) ID: Select_on_dataset_1
[13:17:40] Running: samtools faidx reference/ref.fa 2>> snps.log
[13:17:40] Running: bwa index reference/ref.fa 2>> snps.log
[13:17:43] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[13:17:43] Running: ln -sf reference/ref.fa . 2>> snps.log
[13:17:43] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[13:17:43] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[13:17:43] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_1\tSM:Select_on_dataset_1' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72274648/inputs/dataset_2fc7b817-f05e-4fd8-bc46-5fee29524df4.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72274648/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72274648/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72274648/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::process] read 2 sequences (9782257 bp)...
[M::mem_process_seqs] Processed 2 rea |
| 1 | [14:38:58] This is snippy 4.6.0Show full stderr[14:38:58] This is snippy 4.6.0
[14:38:58] Written by Torsten Seemann
[14:38:58] Obtained from https://github.com/tseemann/snippy
[14:38:58] Detected operating system: linux
[14:38:58] Enabling bundled linux tools.
[14:38:58] Found bwa - /usr/local/bin/bwa
[14:38:58] Found bcftools - /usr/local/bin/bcftools
[14:38:58] Found samtools - /usr/local/bin/samtools
[14:38:58] Found java - /usr/local/bin/java
[14:38:58] Found snpEff - /usr/local/bin/snpEff
[14:38:58] Found samclip - /usr/local/bin/samclip
[14:38:58] Found seqtk - /usr/local/bin/seqtk
[14:38:58] Found parallel - /usr/local/bin/parallel
[14:38:58] Found freebayes - /usr/local/bin/freebayes
[14:38:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:38:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:38:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:38:58] Found vcfuniq - /usr/local/bin/vcfuniq
[14:38:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:38:58] Found gzip - /bin/gzip
[14:38:58] Found vt - /usr/local/bin/vt
[14:38:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:38:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:38:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:38:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:38:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:38:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:38:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:38:58] Using reference: /jetstream2/scratch/main/jobs/72276988/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat
[14:38:59] Treating reference as 'fasta' format.
[14:38:59] Will use 1 CPU cores.
[14:38:59] Using read file: /jetstream2/scratch/main/jobs/72276988/inputs/dataset_528cab5d-bce5-4533-80c7-807895d7ede6.dat
[14:38:59] Creating folder: Select_on_dataset_10
[14:38:59] Changing working directory: Select_on_dataset_10
[14:38:59] Creating reference folder: reference
[14:38:59] Extracting FASTA and GFF from reference.
[14:38:59] Wrote 3 sequences to ref.fa
[14:38:59] Wrote 0 features to ref.gff
[14:38:59] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[14:38:59] Using BAM RG (Read Group) ID: Select_on_dataset_10
[14:38:59] Running: samtools faidx reference/ref.fa 2>> snps.log
[14:38:59] Running: bwa index reference/ref.fa 2>> snps.log
[14:39:02] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[14:39:02] Running: ln -sf reference/ref.fa . 2>> snps.log
[14:39:02] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[14:39:02] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[14:39:02] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_10\tSM:Select_on_dataset_10' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72276988/inputs/dataset_528cab5d-bce5-4533-80c7-807895d7ede6.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72276988/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72276988/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72276988/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::process] read 1 sequences (10262635 bp)...
[M::mem_process_seqs] Processed |
| 1 | [14:43:57] This is snippy 4.6.0Show full stderr[14:43:57] This is snippy 4.6.0
[14:43:57] Written by Torsten Seemann
[14:43:57] Obtained from https://github.com/tseemann/snippy
[14:43:57] Detected operating system: linux
[14:43:57] Enabling bundled linux tools.
[14:43:57] Found bwa - /usr/local/bin/bwa
[14:43:57] Found bcftools - /usr/local/bin/bcftools
[14:43:57] Found samtools - /usr/local/bin/samtools
[14:43:57] Found java - /usr/local/bin/java
[14:43:57] Found snpEff - /usr/local/bin/snpEff
[14:43:57] Found samclip - /usr/local/bin/samclip
[14:43:57] Found seqtk - /usr/local/bin/seqtk
[14:43:57] Found parallel - /usr/local/bin/parallel
[14:43:57] Found freebayes - /usr/local/bin/freebayes
[14:43:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:43:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:43:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:43:57] Found vcfuniq - /usr/local/bin/vcfuniq
[14:43:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:43:57] Found gzip - /bin/gzip
[14:43:57] Found vt - /usr/local/bin/vt
[14:43:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:43:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:43:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:43:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:43:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:43:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:43:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:43:58] Using reference: /jetstream2/scratch/main/jobs/72276992/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat
[14:43:58] Treating reference as 'fasta' format.
[14:43:58] Will use 1 CPU cores.
[14:43:58] Using read file: /jetstream2/scratch/main/jobs/72276992/inputs/dataset_721aefd6-f7c7-4a1b-96ab-de8d3a958004.dat
[14:43:58] Creating folder: Select_on_dataset_15
[14:43:58] Changing working directory: Select_on_dataset_15
[14:43:58] Creating reference folder: reference
[14:43:58] Extracting FASTA and GFF from reference.
[14:43:59] Wrote 3 sequences to ref.fa
[14:43:59] Wrote 0 features to ref.gff
[14:43:59] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[14:43:59] Using BAM RG (Read Group) ID: Select_on_dataset_15
[14:43:59] Running: samtools faidx reference/ref.fa 2>> snps.log
[14:43:59] Running: bwa index reference/ref.fa 2>> snps.log
[14:44:02] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[14:44:02] Running: ln -sf reference/ref.fa . 2>> snps.log
[14:44:02] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[14:44:02] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[14:44:02] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_15\tSM:Select_on_dataset_15' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72276992/inputs/dataset_721aefd6-f7c7-4a1b-96ab-de8d3a958004.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72276992/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72276992/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72276992/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::process] read 1 sequences (10101518 bp)...
[M::mem_process_seqs] Processed |
| 1 | [14:46:53] This is snippy 4.6.0Show full stderr[14:46:53] This is snippy 4.6.0
[14:46:53] Written by Torsten Seemann
[14:46:53] Obtained from https://github.com/tseemann/snippy
[14:46:53] Detected operating system: linux
[14:46:53] Enabling bundled linux tools.
[14:46:53] Found bwa - /usr/local/bin/bwa
[14:46:53] Found bcftools - /usr/local/bin/bcftools
[14:46:53] Found samtools - /usr/local/bin/samtools
[14:46:53] Found java - /usr/local/bin/java
[14:46:53] Found snpEff - /usr/local/bin/snpEff
[14:46:53] Found samclip - /usr/local/bin/samclip
[14:46:53] Found seqtk - /usr/local/bin/seqtk
[14:46:53] Found parallel - /usr/local/bin/parallel
[14:46:53] Found freebayes - /usr/local/bin/freebayes
[14:46:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:53] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:53] Found gzip - /bin/gzip
[14:46:53] Found vt - /usr/local/bin/vt
[14:46:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:54] Using reference: /jetstream2/scratch/main/jobs/72276995/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat
[14:46:54] Treating reference as 'fasta' format.
[14:46:54] Will use 1 CPU cores.
[14:46:54] Using read file: /jetstream2/scratch/main/jobs/72276995/inputs/dataset_20845546-a649-4a94-aa76-3444d7ff9ff5.dat
[14:46:54] Creating folder: Select_on_dataset_18
[14:46:54] Changing working directory: Select_on_dataset_18
[14:46:54] Creating reference folder: reference
[14:46:54] Extracting FASTA and GFF from reference.
[14:46:55] Wrote 3 sequences to ref.fa
[14:46:55] Wrote 0 features to ref.gff
[14:46:55] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[14:46:55] Using BAM RG (Read Group) ID: Select_on_dataset_18
[14:46:55] Running: samtools faidx reference/ref.fa 2>> snps.log
[14:46:55] Running: bwa index reference/ref.fa 2>> snps.log
[14:46:58] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[14:46:59] Running: ln -sf reference/ref.fa . 2>> snps.log
[14:46:59] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[14:46:59] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[14:46:59] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_18\tSM:Select_on_dataset_18' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72276995/inputs/dataset_20845546-a649-4a94-aa76-3444d7ff9ff5.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72276995/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72276995/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72276995/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::process] read 3 sequences (9598041 bp)...
[M::mem_process_seqs] Processed 3 |
| 1 | [14:36:13] This is snippy 4.6.0Show full stderr[14:36:13] This is snippy 4.6.0
[14:36:13] Written by Torsten Seemann
[14:36:13] Obtained from https://github.com/tseemann/snippy
[14:36:13] Detected operating system: linux
[14:36:13] Enabling bundled linux tools.
[14:36:14] Found bwa - /usr/local/bin/bwa
[14:36:14] Found bcftools - /usr/local/bin/bcftools
[14:36:14] Found samtools - /usr/local/bin/samtools
[14:36:14] Found java - /usr/local/bin/java
[14:36:14] Found snpEff - /usr/local/bin/snpEff
[14:36:14] Found samclip - /usr/local/bin/samclip
[14:36:14] Found seqtk - /usr/local/bin/seqtk
[14:36:14] Found parallel - /usr/local/bin/parallel
[14:36:14] Found freebayes - /usr/local/bin/freebayes
[14:36:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:36:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:36:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:36:14] Found vcfuniq - /usr/local/bin/vcfuniq
[14:36:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:36:14] Found gzip - /bin/gzip
[14:36:14] Found vt - /usr/local/bin/vt
[14:36:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:36:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:36:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:36:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:36:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:36:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:36:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:36:14] Using reference: /jetstream2/scratch/main/jobs/72277004/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat
[14:36:14] Treating reference as 'fasta' format.
[14:36:14] Will use 1 CPU cores.
[14:36:14] Using read file: /jetstream2/scratch/main/jobs/72277004/inputs/dataset_88444cf6-27f7-44aa-93a7-00a38bdbf1f8.dat
[14:36:14] Creating folder: Select_on_dataset_28
[14:36:14] Changing working directory: Select_on_dataset_28
[14:36:14] Creating reference folder: reference
[14:36:14] Extracting FASTA and GFF from reference.
[14:36:15] Wrote 3 sequences to ref.fa
[14:36:15] Wrote 0 features to ref.gff
[14:36:15] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[14:36:15] Using BAM RG (Read Group) ID: Select_on_dataset_28
[14:36:15] Running: samtools faidx reference/ref.fa 2>> snps.log
[14:36:15] Running: bwa index reference/ref.fa 2>> snps.log
[14:36:18] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[14:36:18] Running: ln -sf reference/ref.fa . 2>> snps.log
[14:36:18] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[14:36:18] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[14:36:18] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_28\tSM:Select_on_dataset_28' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72277004/inputs/dataset_88444cf6-27f7-44aa-93a7-00a38bdbf1f8.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72277004/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72277004/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72277004/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::process] read 1 sequences (12213033 bp)...
[M::mem_process_seqs] Processed |
| 1 | [17:50:23] This is snippy 4.6.0Show full stderr[17:50:23] This is snippy 4.6.0
[17:50:23] Written by Torsten Seemann
[17:50:23] Obtained from https://github.com/tseemann/snippy
[17:50:23] Detected operating system: linux
[17:50:23] Enabling bundled linux tools.
[17:50:23] Found bwa - /usr/local/bin/bwa
[17:50:23] Found bcftools - /usr/local/bin/bcftools
[17:50:23] Found samtools - /usr/local/bin/samtools
[17:50:23] Found java - /usr/local/bin/java
[17:50:23] Found snpEff - /usr/local/bin/snpEff
[17:50:23] Found samclip - /usr/local/bin/samclip
[17:50:23] Found seqtk - /usr/local/bin/seqtk
[17:50:23] Found parallel - /usr/local/bin/parallel
[17:50:23] Found freebayes - /usr/local/bin/freebayes
[17:50:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:50:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:50:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:50:23] Found vcfuniq - /usr/local/bin/vcfuniq
[17:50:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:50:23] Found gzip - /bin/gzip
[17:50:23] Found vt - /usr/local/bin/vt
[17:50:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:50:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:50:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:50:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:50:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:50:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:50:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:50:24] Using reference: /jetstream2/scratch/main/jobs/72283434/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat
[17:50:24] Treating reference as 'fasta' format.
[17:50:24] Will use 1 CPU cores.
[17:50:24] Using read file: /jetstream2/scratch/main/jobs/72283434/inputs/dataset_20845546-a649-4a94-aa76-3444d7ff9ff5.dat
[17:50:24] Creating folder: Select_on_dataset_18
[17:50:24] Changing working directory: Select_on_dataset_18
[17:50:24] Creating reference folder: reference
[17:50:24] Extracting FASTA and GFF from reference.
[17:50:25] Wrote 3 sequences to ref.fa
[17:50:25] Wrote 0 features to ref.gff
[17:50:25] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[17:50:25] Using BAM RG (Read Group) ID: Select_on_dataset_18
[17:50:25] Running: samtools faidx reference/ref.fa 2>> snps.log
[17:50:25] Running: bwa index reference/ref.fa 2>> snps.log
[17:50:28] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[17:50:29] Running: ln -sf reference/ref.fa . 2>> snps.log
[17:50:29] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[17:50:29] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[17:50:29] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_18\tSM:Select_on_dataset_18' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72283434/inputs/dataset_20845546-a649-4a94-aa76-3444d7ff9ff5.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72283434/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72283434/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72283434/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 3 sequences in reference/ref.fa.fai
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 3 sequences (9598041 bp)...
[M::mem_process_seqs] Processed 3 |
| 1 | [19:30:05] This is snippy 4.6.0Show full stderr[19:30:05] This is snippy 4.6.0
[19:30:05] Written by Torsten Seemann
[19:30:05] Obtained from https://github.com/tseemann/snippy
[19:30:05] Detected operating system: linux
[19:30:05] Enabling bundled linux tools.
[19:30:05] Found bwa - /usr/local/bin/bwa
[19:30:05] Found bcftools - /usr/local/bin/bcftools
[19:30:05] Found samtools - /usr/local/bin/samtools
[19:30:05] Found java - /usr/local/bin/java
[19:30:05] Found snpEff - /usr/local/bin/snpEff
[19:30:05] Found samclip - /usr/local/bin/samclip
[19:30:05] Found seqtk - /usr/local/bin/seqtk
[19:30:05] Found parallel - /usr/local/bin/parallel
[19:30:05] Found freebayes - /usr/local/bin/freebayes
[19:30:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:30:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:30:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:30:05] Found vcfuniq - /usr/local/bin/vcfuniq
[19:30:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:30:05] Found gzip - /bin/gzip
[19:30:05] Found vt - /usr/local/bin/vt
[19:30:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:30:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:30:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:30:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:30:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:30:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:30:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:30:06] Using reference: /corral4/main/objects/d/2/b/dataset_d2be515a-eac5-47a6-9e5f-c856da7a145f.dat
[19:30:06] Could not guess format '/corral4/main/objects/d/2/b/dataset_d2be515a-eac5-47a6-9e5f-c856da7a145f.dat' |
| 1 | [04:43:25] This is snippy 4.6.0Show full stderr[04:43:25] This is snippy 4.6.0
[04:43:25] Written by Torsten Seemann
[04:43:25] Obtained from https://github.com/tseemann/snippy
[04:43:25] Detected operating system: linux
[04:43:25] Enabling bundled linux tools.
[04:43:25] Found bwa - /usr/local/bin/bwa
[04:43:25] Found bcftools - /usr/local/bin/bcftools
[04:43:25] Found samtools - /usr/local/bin/samtools
[04:43:25] Found java - /usr/local/bin/java
[04:43:25] Found snpEff - /usr/local/bin/snpEff
[04:43:25] Found samclip - /usr/local/bin/samclip
[04:43:25] Found seqtk - /usr/local/bin/seqtk
[04:43:25] Found parallel - /usr/local/bin/parallel
[04:43:25] Found freebayes - /usr/local/bin/freebayes
[04:43:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:25] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:25] Found gzip - /bin/gzip
[04:43:25] Found vt - /usr/local/bin/vt
[04:43:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:45] This is snippy 4.6.0Show full stderr[04:43:45] This is snippy 4.6.0
[04:43:45] Written by Torsten Seemann
[04:43:45] Obtained from https://github.com/tseemann/snippy
[04:43:45] Detected operating system: linux
[04:43:45] Enabling bundled linux tools.
[04:43:45] Found bwa - /usr/local/bin/bwa
[04:43:45] Found bcftools - /usr/local/bin/bcftools
[04:43:45] Found samtools - /usr/local/bin/samtools
[04:43:45] Found java - /usr/local/bin/java
[04:43:45] Found snpEff - /usr/local/bin/snpEff
[04:43:45] Found samclip - /usr/local/bin/samclip
[04:43:45] Found seqtk - /usr/local/bin/seqtk
[04:43:45] Found parallel - /usr/local/bin/parallel
[04:43:45] Found freebayes - /usr/local/bin/freebayes
[04:43:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:45] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:45] Found gzip - /bin/gzip
[04:43:45] Found vt - /usr/local/bin/vt
[04:43:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:36] This is snippy 4.6.0Show full stderr[04:43:36] This is snippy 4.6.0
[04:43:36] Written by Torsten Seemann
[04:43:36] Obtained from https://github.com/tseemann/snippy
[04:43:36] Detected operating system: linux
[04:43:36] Enabling bundled linux tools.
[04:43:36] Found bwa - /usr/local/bin/bwa
[04:43:36] Found bcftools - /usr/local/bin/bcftools
[04:43:36] Found samtools - /usr/local/bin/samtools
[04:43:36] Found java - /usr/local/bin/java
[04:43:37] Found snpEff - /usr/local/bin/snpEff
[04:43:37] Found samclip - /usr/local/bin/samclip
[04:43:37] Found seqtk - /usr/local/bin/seqtk
[04:43:37] Found parallel - /usr/local/bin/parallel
[04:43:37] Found freebayes - /usr/local/bin/freebayes
[04:43:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:37] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:37] Found gzip - /bin/gzip
[04:43:37] Found vt - /usr/local/bin/vt
[04:43:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:39] This is snippy 4.6.0Show full stderr[04:43:39] This is snippy 4.6.0
[04:43:39] Written by Torsten Seemann
[04:43:39] Obtained from https://github.com/tseemann/snippy
[04:43:39] Detected operating system: linux
[04:43:39] Enabling bundled linux tools.
[04:43:39] Found bwa - /usr/local/bin/bwa
[04:43:39] Found bcftools - /usr/local/bin/bcftools
[04:43:39] Found samtools - /usr/local/bin/samtools
[04:43:39] Found java - /usr/local/bin/java
[04:43:39] Found snpEff - /usr/local/bin/snpEff
[04:43:39] Found samclip - /usr/local/bin/samclip
[04:43:39] Found seqtk - /usr/local/bin/seqtk
[04:43:39] Found parallel - /usr/local/bin/parallel
[04:43:39] Found freebayes - /usr/local/bin/freebayes
[04:43:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:39] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:39] Found gzip - /bin/gzip
[04:43:39] Found vt - /usr/local/bin/vt
[04:43:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:43] This is snippy 4.6.0Show full stderr[04:43:43] This is snippy 4.6.0
[04:43:43] Written by Torsten Seemann
[04:43:43] Obtained from https://github.com/tseemann/snippy
[04:43:43] Detected operating system: linux
[04:43:43] Enabling bundled linux tools.
[04:43:43] Found bwa - /usr/local/bin/bwa
[04:43:43] Found bcftools - /usr/local/bin/bcftools
[04:43:43] Found samtools - /usr/local/bin/samtools
[04:43:43] Found java - /usr/local/bin/java
[04:43:43] Found snpEff - /usr/local/bin/snpEff
[04:43:43] Found samclip - /usr/local/bin/samclip
[04:43:43] Found seqtk - /usr/local/bin/seqtk
[04:43:43] Found parallel - /usr/local/bin/parallel
[04:43:43] Found freebayes - /usr/local/bin/freebayes
[04:43:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:43] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:43] Found gzip - /bin/gzip
[04:43:43] Found vt - /usr/local/bin/vt
[04:43:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:57] This is snippy 4.6.0Show full stderr[04:43:57] This is snippy 4.6.0
[04:43:57] Written by Torsten Seemann
[04:43:57] Obtained from https://github.com/tseemann/snippy
[04:43:57] Detected operating system: linux
[04:43:57] Enabling bundled linux tools.
[04:43:57] Found bwa - /usr/local/bin/bwa
[04:43:57] Found bcftools - /usr/local/bin/bcftools
[04:43:57] Found samtools - /usr/local/bin/samtools
[04:43:57] Found java - /usr/local/bin/java
[04:43:57] Found snpEff - /usr/local/bin/snpEff
[04:43:57] Found samclip - /usr/local/bin/samclip
[04:43:57] Found seqtk - /usr/local/bin/seqtk
[04:43:57] Found parallel - /usr/local/bin/parallel
[04:43:57] Found freebayes - /usr/local/bin/freebayes
[04:43:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:57] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:57] Found gzip - /bin/gzip
[04:43:57] Found vt - /usr/local/bin/vt
[04:43:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:44:02] This is snippy 4.6.0Show full stderr[04:44:02] This is snippy 4.6.0
[04:44:02] Written by Torsten Seemann
[04:44:02] Obtained from https://github.com/tseemann/snippy
[04:44:02] Detected operating system: linux
[04:44:02] Enabling bundled linux tools.
[04:44:02] Found bwa - /usr/local/bin/bwa
[04:44:02] Found bcftools - /usr/local/bin/bcftools
[04:44:02] Found samtools - /usr/local/bin/samtools
[04:44:02] Found java - /usr/local/bin/java
[04:44:02] Found snpEff - /usr/local/bin/snpEff
[04:44:02] Found samclip - /usr/local/bin/samclip
[04:44:02] Found seqtk - /usr/local/bin/seqtk
[04:44:02] Found parallel - /usr/local/bin/parallel
[04:44:02] Found freebayes - /usr/local/bin/freebayes
[04:44:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:44:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:44:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:44:02] Found vcfuniq - /usr/local/bin/vcfuniq
[04:44:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:44:02] Found gzip - /bin/gzip
[04:44:02] Found vt - /usr/local/bin/vt
[04:44:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:44:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:44:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:44:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:44:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:44:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:44:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:44:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:49:36] This is snippy 4.6.0Show full stderr[04:49:36] This is snippy 4.6.0
[04:49:36] Written by Torsten Seemann
[04:49:36] Obtained from https://github.com/tseemann/snippy
[04:49:36] Detected operating system: linux
[04:49:36] Enabling bundled linux tools.
[04:49:36] Found bwa - /usr/local/bin/bwa
[04:49:36] Found bcftools - /usr/local/bin/bcftools
[04:49:36] Found samtools - /usr/local/bin/samtools
[04:49:36] Found java - /usr/local/bin/java
[04:49:36] Found snpEff - /usr/local/bin/snpEff
[04:49:36] Found samclip - /usr/local/bin/samclip
[04:49:36] Found seqtk - /usr/local/bin/seqtk
[04:49:36] Found parallel - /usr/local/bin/parallel
[04:49:36] Found freebayes - /usr/local/bin/freebayes
[04:49:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:49:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:49:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:49:36] Found vcfuniq - /usr/local/bin/vcfuniq
[04:49:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:49:36] Found gzip - /bin/gzip
[04:49:36] Found vt - /usr/local/bin/vt
[04:49:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:49:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:49:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:49:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:49:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:49:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:49:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:49:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:49:51] This is snippy 4.6.0Show full stderr[04:49:51] This is snippy 4.6.0
[04:49:51] Written by Torsten Seemann
[04:49:51] Obtained from https://github.com/tseemann/snippy
[04:49:51] Detected operating system: linux
[04:49:51] Enabling bundled linux tools.
[04:49:51] Found bwa - /usr/local/bin/bwa
[04:49:51] Found bcftools - /usr/local/bin/bcftools
[04:49:51] Found samtools - /usr/local/bin/samtools
[04:49:51] Found java - /usr/local/bin/java
[04:49:51] Found snpEff - /usr/local/bin/snpEff
[04:49:51] Found samclip - /usr/local/bin/samclip
[04:49:51] Found seqtk - /usr/local/bin/seqtk
[04:49:51] Found parallel - /usr/local/bin/parallel
[04:49:51] Found freebayes - /usr/local/bin/freebayes
[04:49:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:49:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:49:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:49:51] Found vcfuniq - /usr/local/bin/vcfuniq
[04:49:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:49:51] Found gzip - /bin/gzip
[04:49:51] Found vt - /usr/local/bin/vt
[04:49:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:49:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:49:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:49:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:49:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:49:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:49:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:49:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [04:43:32] This is snippy 4.6.0Show full stderr[04:43:32] This is snippy 4.6.0
[04:43:32] Written by Torsten Seemann
[04:43:32] Obtained from https://github.com/tseemann/snippy
[04:43:32] Detected operating system: linux
[04:43:32] Enabling bundled linux tools.
[04:43:32] Found bwa - /usr/local/bin/bwa
[04:43:32] Found bcftools - /usr/local/bin/bcftools
[04:43:32] Found samtools - /usr/local/bin/samtools
[04:43:32] Found java - /usr/local/bin/java
[04:43:32] Found snpEff - /usr/local/bin/snpEff
[04:43:32] Found samclip - /usr/local/bin/samclip
[04:43:32] Found seqtk - /usr/local/bin/seqtk
[04:43:32] Found parallel - /usr/local/bin/parallel
[04:43:32] Found freebayes - /usr/local/bin/freebayes
[04:43:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[04:43:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[04:43:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[04:43:32] Found vcfuniq - /usr/local/bin/vcfuniq
[04:43:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[04:43:32] Found gzip - /bin/gzip
[04:43:32] Found vt - /usr/local/bin/vt
[04:43:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[04:43:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[04:43:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[04:43:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[04:43:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[04:43:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[04:43:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[04:43:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [10:24:53] This is snippy 4.6.0Show full stderr[10:24:53] This is snippy 4.6.0
[10:24:53] Written by Torsten Seemann
[10:24:53] Obtained from https://github.com/tseemann/snippy
[10:24:53] Detected operating system: linux
[10:24:53] Enabling bundled linux tools.
[10:24:53] Found bwa - /usr/local/bin/bwa
[10:24:53] Found bcftools - /usr/local/bin/bcftools
[10:24:53] Found samtools - /usr/local/bin/samtools
[10:24:53] Found java - /usr/local/bin/java
[10:24:53] Found snpEff - /usr/local/bin/snpEff
[10:24:53] Found samclip - /usr/local/bin/samclip
[10:24:53] Found seqtk - /usr/local/bin/seqtk
[10:24:53] Found parallel - /usr/local/bin/parallel
[10:24:53] Found freebayes - /usr/local/bin/freebayes
[10:24:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:24:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:24:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:24:53] Found vcfuniq - /usr/local/bin/vcfuniq
[10:24:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:24:53] Found gzip - /bin/gzip
[10:24:53] Found vt - /usr/local/bin/vt
[10:24:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:24:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:24:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:24:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:24:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:24:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:24:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:24:54] Using reference: /corral4/main/objects/2/6/3/dataset_2633c7de-ac59-4614-a6e1-1b68720a214a.dat
[10:24:54] Treating reference as 'genbank' format.
[10:24:54] Will use 1 CPU cores.
[10:24:54] Using read file: /corral4/main/objects/7/c/7/dataset_7c76c421-2e73-43c8-a760-8db79445644b.dat
[10:24:54] Creating folder: GCA_009734005_2_ASM973400v2_genomic_fna
[10:24:54] Changing working directory: GCA_009734005_2_ASM973400v2_genomic_fna
[10:24:54] Creating reference folder: reference
[10:24:54] Extracting FASTA and GFF from reference.
[10:24:55] Wrote 1 sequences to ref.fa
[10:24:55] Wrote 1 features to ref.gff
[10:24:55] Shredding /corral4/main/objects/7/c/7/dataset_7c76c421-2e73-43c8-a760-8db79445644b.dat into pseudo-reads
[10:24:57] Wrote 233618 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[10:24:57] Creating reference/snpeff.config
[10:24:57] Freebayes will process 1 chunks of 2951188 bp, 1 chunks at a time.
[10:24:57] Using BAM RG (Read Group) ID: GCA_009734005_2_ASM973400v2_genomic_fna
[10:24:57] Running: samtools faidx reference/ref.fa 2>> snps.log
[10:24:57] Running: bwa index reference/ref.fa 2>> snps.log
[10:24:58] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[10:24:58] Running: ln -sf reference/ref.fa . 2>> snps.log
[10:24:58] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[10:24:58] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[10:24:58] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[10:25:01] Error running command, check GCA_009734005_2_ASM973400v2_genomic_fna/snps.log |
| 1 | [13:49:16] This is snippy 4.6.0Show full stderr[13:49:16] This is snippy 4.6.0
[13:49:16] Written by Torsten Seemann
[13:49:16] Obtained from https://github.com/tseemann/snippy
[13:49:16] Detected operating system: linux
[13:49:16] Enabling bundled linux tools.
[13:49:16] Found bwa - /usr/local/bin/bwa
[13:49:16] Found bcftools - /usr/local/bin/bcftools
[13:49:16] Found samtools - /usr/local/bin/samtools
[13:49:16] Found java - /usr/local/bin/java
[13:49:16] Found snpEff - /usr/local/bin/snpEff
[13:49:16] Found samclip - /usr/local/bin/samclip
[13:49:16] Found seqtk - /usr/local/bin/seqtk
[13:49:16] Found parallel - /usr/local/bin/parallel
[13:49:16] Found freebayes - /usr/local/bin/freebayes
[13:49:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:49:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:49:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:49:16] Found vcfuniq - /usr/local/bin/vcfuniq
[13:49:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:49:16] Found gzip - /bin/gzip
[13:49:16] Found vt - /usr/local/bin/vt
[13:49:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:49:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:49:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:49:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:49:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:49:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:49:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:49:17] Using reference: /jetstream2/scratch/main/jobs/72310760/inputs/dataset_c3278295-0534-4341-a983-519e27d93d98.dat
[13:49:17] Treating reference as 'fasta' format.
[13:49:17] Will use 1 CPU cores.
[13:49:17] Using read file: /jetstream2/scratch/main/jobs/72310760/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat
[13:49:17] Creating folder: Select_on_dataset_11
[13:49:17] Changing working directory: Select_on_dataset_11
[13:49:17] Creating reference folder: reference
[13:49:17] Extracting FASTA and GFF from reference.
[13:49:17] Wrote 1 sequences to ref.fa
[13:49:17] Wrote 0 features to ref.gff
[13:49:17] Freebayes will process 1 chunks of 12416664 bp, 1 chunks at a time.
[13:49:17] Using BAM RG (Read Group) ID: Select_on_dataset_11
[13:49:17] Running: samtools faidx reference/ref.fa 2>> snps.log
[13:49:18] Running: bwa index reference/ref.fa 2>> snps.log
[13:49:23] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[13:49:23] Running: ln -sf reference/ref.fa . 2>> snps.log
[13:49:23] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[13:49:23] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[13:49:23] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_11\tSM:Select_on_dataset_11' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72310760/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72310760/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72310760/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72310760/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences in reference/ref.fa.fai
[M::process] read 1 sequences (11639536 bp)...
[samclip] Total SAM records 0 |
| 1 | [09:46:52] This is snippy 4.6.0Show full stderr[09:46:52] This is snippy 4.6.0
[09:46:52] Written by Torsten Seemann
[09:46:52] Obtained from https://github.com/tseemann/snippy
[09:46:52] Detected operating system: linux
[09:46:52] Enabling bundled linux tools.
[09:46:52] Found bwa - /usr/local/bin/bwa
[09:46:52] Found bcftools - /usr/local/bin/bcftools
[09:46:52] Found samtools - /usr/local/bin/samtools
[09:46:52] Found java - /usr/local/bin/java
[09:46:52] Found snpEff - /usr/local/bin/snpEff
[09:46:52] Found samclip - /usr/local/bin/samclip
[09:46:52] Found seqtk - /usr/local/bin/seqtk
[09:46:52] Found parallel - /usr/local/bin/parallel
[09:46:52] Found freebayes - /usr/local/bin/freebayes
[09:46:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:46:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:46:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:46:52] Found vcfuniq - /usr/local/bin/vcfuniq
[09:46:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:46:52] Found gzip - /bin/gzip
[09:46:52] Found vt - /usr/local/bin/vt
[09:46:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:46:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:46:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:46:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:46:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:46:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:46:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:46:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [09:46:39] This is snippy 4.6.0Show full stderr[09:46:39] This is snippy 4.6.0
[09:46:39] Written by Torsten Seemann
[09:46:39] Obtained from https://github.com/tseemann/snippy
[09:46:39] Detected operating system: linux
[09:46:39] Enabling bundled linux tools.
[09:46:39] Found bwa - /usr/local/bin/bwa
[09:46:39] Found bcftools - /usr/local/bin/bcftools
[09:46:39] Found samtools - /usr/local/bin/samtools
[09:46:39] Found java - /usr/local/bin/java
[09:46:39] Found snpEff - /usr/local/bin/snpEff
[09:46:39] Found samclip - /usr/local/bin/samclip
[09:46:39] Found seqtk - /usr/local/bin/seqtk
[09:46:39] Found parallel - /usr/local/bin/parallel
[09:46:39] Found freebayes - /usr/local/bin/freebayes
[09:46:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:46:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:46:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:46:39] Found vcfuniq - /usr/local/bin/vcfuniq
[09:46:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:46:39] Found gzip - /bin/gzip
[09:46:39] Found vt - /usr/local/bin/vt
[09:46:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:46:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:46:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:46:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:46:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:46:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:46:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:46:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:48:30] This is snippy 4.6.0Show full stderr[12:48:30] This is snippy 4.6.0
[12:48:30] Written by Torsten Seemann
[12:48:30] Obtained from https://github.com/tseemann/snippy
[12:48:30] Detected operating system: linux
[12:48:30] Enabling bundled linux tools.
[12:48:30] Found bwa - /usr/local/bin/bwa
[12:48:30] Found bcftools - /usr/local/bin/bcftools
[12:48:30] Found samtools - /usr/local/bin/samtools
[12:48:30] Found java - /usr/local/bin/java
[12:48:30] Found snpEff - /usr/local/bin/snpEff
[12:48:30] Found samclip - /usr/local/bin/samclip
[12:48:30] Found seqtk - /usr/local/bin/seqtk
[12:48:30] Found parallel - /usr/local/bin/parallel
[12:48:30] Found freebayes - /usr/local/bin/freebayes
[12:48:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:48:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:48:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:48:30] Found vcfuniq - /usr/local/bin/vcfuniq
[12:48:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:48:30] Found gzip - /bin/gzip
[12:48:30] Found vt - /usr/local/bin/vt
[12:48:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:48:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:48:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:48:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:48:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:48:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:48:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:48:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:49:18] This is snippy 4.6.0Show full stderr[12:49:18] This is snippy 4.6.0
[12:49:18] Written by Torsten Seemann
[12:49:18] Obtained from https://github.com/tseemann/snippy
[12:49:18] Detected operating system: linux
[12:49:18] Enabling bundled linux tools.
[12:49:18] Found bwa - /usr/local/bin/bwa
[12:49:18] Found bcftools - /usr/local/bin/bcftools
[12:49:18] Found samtools - /usr/local/bin/samtools
[12:49:18] Found java - /usr/local/bin/java
[12:49:18] Found snpEff - /usr/local/bin/snpEff
[12:49:18] Found samclip - /usr/local/bin/samclip
[12:49:18] Found seqtk - /usr/local/bin/seqtk
[12:49:18] Found parallel - /usr/local/bin/parallel
[12:49:18] Found freebayes - /usr/local/bin/freebayes
[12:49:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:49:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:49:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:49:18] Found vcfuniq - /usr/local/bin/vcfuniq
[12:49:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:49:18] Found gzip - /bin/gzip
[12:49:18] Found vt - /usr/local/bin/vt
[12:49:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:49:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:49:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:49:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:49:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:49:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:49:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:49:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:49:21] This is snippy 4.6.0Show full stderr[12:49:21] This is snippy 4.6.0
[12:49:21] Written by Torsten Seemann
[12:49:21] Obtained from https://github.com/tseemann/snippy
[12:49:21] Detected operating system: linux
[12:49:21] Enabling bundled linux tools.
[12:49:21] Found bwa - /usr/local/bin/bwa
[12:49:21] Found bcftools - /usr/local/bin/bcftools
[12:49:21] Found samtools - /usr/local/bin/samtools
[12:49:21] Found java - /usr/local/bin/java
[12:49:21] Found snpEff - /usr/local/bin/snpEff
[12:49:21] Found samclip - /usr/local/bin/samclip
[12:49:21] Found seqtk - /usr/local/bin/seqtk
[12:49:21] Found parallel - /usr/local/bin/parallel
[12:49:21] Found freebayes - /usr/local/bin/freebayes
[12:49:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:49:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:49:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:49:21] Found vcfuniq - /usr/local/bin/vcfuniq
[12:49:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:49:21] Found gzip - /bin/gzip
[12:49:21] Found vt - /usr/local/bin/vt
[12:49:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:49:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:49:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:49:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:49:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:49:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:49:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:49:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:49:33] This is snippy 4.6.0Show full stderr[12:49:33] This is snippy 4.6.0
[12:49:33] Written by Torsten Seemann
[12:49:33] Obtained from https://github.com/tseemann/snippy
[12:49:33] Detected operating system: linux
[12:49:33] Enabling bundled linux tools.
[12:49:33] Found bwa - /usr/local/bin/bwa
[12:49:33] Found bcftools - /usr/local/bin/bcftools
[12:49:33] Found samtools - /usr/local/bin/samtools
[12:49:33] Found java - /usr/local/bin/java
[12:49:33] Found snpEff - /usr/local/bin/snpEff
[12:49:33] Found samclip - /usr/local/bin/samclip
[12:49:33] Found seqtk - /usr/local/bin/seqtk
[12:49:33] Found parallel - /usr/local/bin/parallel
[12:49:33] Found freebayes - /usr/local/bin/freebayes
[12:49:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:49:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:49:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:49:33] Found vcfuniq - /usr/local/bin/vcfuniq
[12:49:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:49:33] Found gzip - /bin/gzip
[12:49:33] Found vt - /usr/local/bin/vt
[12:49:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:49:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:49:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:49:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:49:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:49:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:49:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:49:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:49:45] This is snippy 4.6.0Show full stderr[12:49:45] This is snippy 4.6.0
[12:49:45] Written by Torsten Seemann
[12:49:45] Obtained from https://github.com/tseemann/snippy
[12:49:45] Detected operating system: linux
[12:49:45] Enabling bundled linux tools.
[12:49:45] Found bwa - /usr/local/bin/bwa
[12:49:45] Found bcftools - /usr/local/bin/bcftools
[12:49:45] Found samtools - /usr/local/bin/samtools
[12:49:45] Found java - /usr/local/bin/java
[12:49:45] Found snpEff - /usr/local/bin/snpEff
[12:49:45] Found samclip - /usr/local/bin/samclip
[12:49:45] Found seqtk - /usr/local/bin/seqtk
[12:49:45] Found parallel - /usr/local/bin/parallel
[12:49:45] Found freebayes - /usr/local/bin/freebayes
[12:49:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:49:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:49:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:49:45] Found vcfuniq - /usr/local/bin/vcfuniq
[12:49:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:49:45] Found gzip - /bin/gzip
[12:49:45] Found vt - /usr/local/bin/vt
[12:49:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:49:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:49:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:49:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:49:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:49:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:49:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:49:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:49:48] This is snippy 4.6.0Show full stderr[12:49:48] This is snippy 4.6.0
[12:49:48] Written by Torsten Seemann
[12:49:48] Obtained from https://github.com/tseemann/snippy
[12:49:48] Detected operating system: linux
[12:49:48] Enabling bundled linux tools.
[12:49:48] Found bwa - /usr/local/bin/bwa
[12:49:48] Found bcftools - /usr/local/bin/bcftools
[12:49:48] Found samtools - /usr/local/bin/samtools
[12:49:48] Found java - /usr/local/bin/java
[12:49:48] Found snpEff - /usr/local/bin/snpEff
[12:49:48] Found samclip - /usr/local/bin/samclip
[12:49:48] Found seqtk - /usr/local/bin/seqtk
[12:49:48] Found parallel - /usr/local/bin/parallel
[12:49:48] Found freebayes - /usr/local/bin/freebayes
[12:49:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:49:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:49:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:49:48] Found vcfuniq - /usr/local/bin/vcfuniq
[12:49:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:49:48] Found gzip - /bin/gzip
[12:49:48] Found vt - /usr/local/bin/vt
[12:49:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:49:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:49:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:49:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:49:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:49:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:49:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:49:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:49:58] This is snippy 4.6.0Show full stderr[12:49:58] This is snippy 4.6.0
[12:49:58] Written by Torsten Seemann
[12:49:58] Obtained from https://github.com/tseemann/snippy
[12:49:58] Detected operating system: linux
[12:49:58] Enabling bundled linux tools.
[12:49:58] Found bwa - /usr/local/bin/bwa
[12:49:58] Found bcftools - /usr/local/bin/bcftools
[12:49:58] Found samtools - /usr/local/bin/samtools
[12:49:58] Found java - /usr/local/bin/java
[12:49:58] Found snpEff - /usr/local/bin/snpEff
[12:49:58] Found samclip - /usr/local/bin/samclip
[12:49:58] Found seqtk - /usr/local/bin/seqtk
[12:49:58] Found parallel - /usr/local/bin/parallel
[12:49:58] Found freebayes - /usr/local/bin/freebayes
[12:49:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:49:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:49:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:49:58] Found vcfuniq - /usr/local/bin/vcfuniq
[12:49:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:49:58] Found gzip - /bin/gzip
[12:49:58] Found vt - /usr/local/bin/vt
[12:49:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:49:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:49:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:49:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:49:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:49:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:49:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:49:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:50:01] This is snippy 4.6.0Show full stderr[12:50:01] This is snippy 4.6.0
[12:50:01] Written by Torsten Seemann
[12:50:01] Obtained from https://github.com/tseemann/snippy
[12:50:01] Detected operating system: linux
[12:50:01] Enabling bundled linux tools.
[12:50:01] Found bwa - /usr/local/bin/bwa
[12:50:01] Found bcftools - /usr/local/bin/bcftools
[12:50:01] Found samtools - /usr/local/bin/samtools
[12:50:01] Found java - /usr/local/bin/java
[12:50:01] Found snpEff - /usr/local/bin/snpEff
[12:50:01] Found samclip - /usr/local/bin/samclip
[12:50:01] Found seqtk - /usr/local/bin/seqtk
[12:50:01] Found parallel - /usr/local/bin/parallel
[12:50:01] Found freebayes - /usr/local/bin/freebayes
[12:50:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:50:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:50:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:50:01] Found vcfuniq - /usr/local/bin/vcfuniq
[12:50:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:50:01] Found gzip - /bin/gzip
[12:50:01] Found vt - /usr/local/bin/vt
[12:50:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:50:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:50:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:50:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:50:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:50:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:50:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:50:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:51:06] This is snippy 4.6.0Show full stderr[12:51:06] This is snippy 4.6.0
[12:51:06] Written by Torsten Seemann
[12:51:06] Obtained from https://github.com/tseemann/snippy
[12:51:06] Detected operating system: linux
[12:51:06] Enabling bundled linux tools.
[12:51:06] Found bwa - /usr/local/bin/bwa
[12:51:06] Found bcftools - /usr/local/bin/bcftools
[12:51:06] Found samtools - /usr/local/bin/samtools
[12:51:06] Found java - /usr/local/bin/java
[12:51:06] Found snpEff - /usr/local/bin/snpEff
[12:51:06] Found samclip - /usr/local/bin/samclip
[12:51:06] Found seqtk - /usr/local/bin/seqtk
[12:51:06] Found parallel - /usr/local/bin/parallel
[12:51:06] Found freebayes - /usr/local/bin/freebayes
[12:51:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:51:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:51:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:51:06] Found vcfuniq - /usr/local/bin/vcfuniq
[12:51:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:51:06] Found gzip - /bin/gzip
[12:51:06] Found vt - /usr/local/bin/vt
[12:51:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:51:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:51:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:51:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:51:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:51:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:51:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:51:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:50:38] This is snippy 4.6.0Show full stderr[12:50:38] This is snippy 4.6.0
[12:50:38] Written by Torsten Seemann
[12:50:38] Obtained from https://github.com/tseemann/snippy
[12:50:38] Detected operating system: linux
[12:50:38] Enabling bundled linux tools.
[12:50:38] Found bwa - /usr/local/bin/bwa
[12:50:38] Found bcftools - /usr/local/bin/bcftools
[12:50:38] Found samtools - /usr/local/bin/samtools
[12:50:38] Found java - /usr/local/bin/java
[12:50:38] Found snpEff - /usr/local/bin/snpEff
[12:50:38] Found samclip - /usr/local/bin/samclip
[12:50:38] Found seqtk - /usr/local/bin/seqtk
[12:50:38] Found parallel - /usr/local/bin/parallel
[12:50:38] Found freebayes - /usr/local/bin/freebayes
[12:50:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:50:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:50:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:50:38] Found vcfuniq - /usr/local/bin/vcfuniq
[12:50:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:50:38] Found gzip - /bin/gzip
[12:50:38] Found vt - /usr/local/bin/vt
[12:50:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:50:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:50:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:50:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:50:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:50:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:50:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:50:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:48:33] This is snippy 4.6.0Show full stderr[12:48:33] This is snippy 4.6.0
[12:48:33] Written by Torsten Seemann
[12:48:33] Obtained from https://github.com/tseemann/snippy
[12:48:33] Detected operating system: linux
[12:48:33] Enabling bundled linux tools.
[12:48:33] Found bwa - /usr/local/bin/bwa
[12:48:33] Found bcftools - /usr/local/bin/bcftools
[12:48:33] Found samtools - /usr/local/bin/samtools
[12:48:33] Found java - /usr/local/bin/java
[12:48:33] Found snpEff - /usr/local/bin/snpEff
[12:48:33] Found samclip - /usr/local/bin/samclip
[12:48:33] Found seqtk - /usr/local/bin/seqtk
[12:48:33] Found parallel - /usr/local/bin/parallel
[12:48:33] Found freebayes - /usr/local/bin/freebayes
[12:48:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:48:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:48:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:48:33] Found vcfuniq - /usr/local/bin/vcfuniq
[12:48:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:48:33] Found gzip - /bin/gzip
[12:48:33] Found vt - /usr/local/bin/vt
[12:48:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:48:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:48:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:48:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:48:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:48:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:48:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:48:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:48:00] This is snippy 4.6.0Show full stderr[12:48:00] This is snippy 4.6.0
[12:48:00] Written by Torsten Seemann
[12:48:00] Obtained from https://github.com/tseemann/snippy
[12:48:00] Detected operating system: linux
[12:48:00] Enabling bundled linux tools.
[12:48:00] Found bwa - /usr/local/bin/bwa
[12:48:00] Found bcftools - /usr/local/bin/bcftools
[12:48:00] Found samtools - /usr/local/bin/samtools
[12:48:00] Found java - /usr/local/bin/java
[12:48:00] Found snpEff - /usr/local/bin/snpEff
[12:48:00] Found samclip - /usr/local/bin/samclip
[12:48:00] Found seqtk - /usr/local/bin/seqtk
[12:48:00] Found parallel - /usr/local/bin/parallel
[12:48:00] Found freebayes - /usr/local/bin/freebayes
[12:48:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:48:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:48:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:48:00] Found vcfuniq - /usr/local/bin/vcfuniq
[12:48:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:48:00] Found gzip - /bin/gzip
[12:48:00] Found vt - /usr/local/bin/vt
[12:48:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:48:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:48:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:48:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:48:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:48:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:48:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:48:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:48:49] This is snippy 4.6.0Show full stderr[12:48:49] This is snippy 4.6.0
[12:48:49] Written by Torsten Seemann
[12:48:49] Obtained from https://github.com/tseemann/snippy
[12:48:49] Detected operating system: linux
[12:48:49] Enabling bundled linux tools.
[12:48:49] Found bwa - /usr/local/bin/bwa
[12:48:49] Found bcftools - /usr/local/bin/bcftools
[12:48:49] Found samtools - /usr/local/bin/samtools
[12:48:49] Found java - /usr/local/bin/java
[12:48:49] Found snpEff - /usr/local/bin/snpEff
[12:48:49] Found samclip - /usr/local/bin/samclip
[12:48:49] Found seqtk - /usr/local/bin/seqtk
[12:48:49] Found parallel - /usr/local/bin/parallel
[12:48:49] Found freebayes - /usr/local/bin/freebayes
[12:48:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:48:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:48:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:48:49] Found vcfuniq - /usr/local/bin/vcfuniq
[12:48:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:48:49] Found gzip - /bin/gzip
[12:48:49] Found vt - /usr/local/bin/vt
[12:48:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:48:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:48:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:48:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:48:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:48:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:48:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:48:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:48:40] This is snippy 4.6.0Show full stderr[12:48:40] This is snippy 4.6.0
[12:48:40] Written by Torsten Seemann
[12:48:40] Obtained from https://github.com/tseemann/snippy
[12:48:40] Detected operating system: linux
[12:48:40] Enabling bundled linux tools.
[12:48:40] Found bwa - /usr/local/bin/bwa
[12:48:40] Found bcftools - /usr/local/bin/bcftools
[12:48:40] Found samtools - /usr/local/bin/samtools
[12:48:40] Found java - /usr/local/bin/java
[12:48:40] Found snpEff - /usr/local/bin/snpEff
[12:48:40] Found samclip - /usr/local/bin/samclip
[12:48:40] Found seqtk - /usr/local/bin/seqtk
[12:48:40] Found parallel - /usr/local/bin/parallel
[12:48:40] Found freebayes - /usr/local/bin/freebayes
[12:48:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:48:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:48:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:48:40] Found vcfuniq - /usr/local/bin/vcfuniq
[12:48:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:48:40] Found gzip - /bin/gzip
[12:48:40] Found vt - /usr/local/bin/vt
[12:48:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:48:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:48:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:48:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:48:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:48:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:48:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:48:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:50:18] This is snippy 4.6.0Show full stderr[12:50:18] This is snippy 4.6.0
[12:50:18] Written by Torsten Seemann
[12:50:18] Obtained from https://github.com/tseemann/snippy
[12:50:18] Detected operating system: linux
[12:50:18] Enabling bundled linux tools.
[12:50:18] Found bwa - /usr/local/bin/bwa
[12:50:18] Found bcftools - /usr/local/bin/bcftools
[12:50:18] Found samtools - /usr/local/bin/samtools
[12:50:18] Found java - /usr/local/bin/java
[12:50:18] Found snpEff - /usr/local/bin/snpEff
[12:50:18] Found samclip - /usr/local/bin/samclip
[12:50:18] Found seqtk - /usr/local/bin/seqtk
[12:50:18] Found parallel - /usr/local/bin/parallel
[12:50:18] Found freebayes - /usr/local/bin/freebayes
[12:50:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:50:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:50:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:50:18] Found vcfuniq - /usr/local/bin/vcfuniq
[12:50:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:50:18] Found gzip - /bin/gzip
[12:50:18] Found vt - /usr/local/bin/vt
[12:50:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:50:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:50:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:50:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:50:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:50:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:50:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:50:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:49:01] This is snippy 4.6.0Show full stderr[12:49:01] This is snippy 4.6.0
[12:49:01] Written by Torsten Seemann
[12:49:01] Obtained from https://github.com/tseemann/snippy
[12:49:01] Detected operating system: linux
[12:49:01] Enabling bundled linux tools.
[12:49:01] Found bwa - /usr/local/bin/bwa
[12:49:01] Found bcftools - /usr/local/bin/bcftools
[12:49:01] Found samtools - /usr/local/bin/samtools
[12:49:01] Found java - /usr/local/bin/java
[12:49:01] Found snpEff - /usr/local/bin/snpEff
[12:49:01] Found samclip - /usr/local/bin/samclip
[12:49:01] Found seqtk - /usr/local/bin/seqtk
[12:49:01] Found parallel - /usr/local/bin/parallel
[12:49:01] Found freebayes - /usr/local/bin/freebayes
[12:49:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:49:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:49:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:49:01] Found vcfuniq - /usr/local/bin/vcfuniq
[12:49:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:49:01] Found gzip - /bin/gzip
[12:49:01] Found vt - /usr/local/bin/vt
[12:49:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:49:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:49:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:49:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:49:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:49:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:49:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:49:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:49:39] This is snippy 4.6.0Show full stderr[12:49:39] This is snippy 4.6.0
[12:49:39] Written by Torsten Seemann
[12:49:39] Obtained from https://github.com/tseemann/snippy
[12:49:39] Detected operating system: linux
[12:49:39] Enabling bundled linux tools.
[12:49:39] Found bwa - /usr/local/bin/bwa
[12:49:39] Found bcftools - /usr/local/bin/bcftools
[12:49:39] Found samtools - /usr/local/bin/samtools
[12:49:39] Found java - /usr/local/bin/java
[12:49:39] Found snpEff - /usr/local/bin/snpEff
[12:49:39] Found samclip - /usr/local/bin/samclip
[12:49:39] Found seqtk - /usr/local/bin/seqtk
[12:49:39] Found parallel - /usr/local/bin/parallel
[12:49:39] Found freebayes - /usr/local/bin/freebayes
[12:49:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:49:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:49:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:49:39] Found vcfuniq - /usr/local/bin/vcfuniq
[12:49:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:49:39] Found gzip - /bin/gzip
[12:49:39] Found vt - /usr/local/bin/vt
[12:49:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:49:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:49:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:49:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:49:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:49:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:49:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:49:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:56:47] This is snippy 4.6.0Show full stderr[12:56:47] This is snippy 4.6.0
[12:56:47] Written by Torsten Seemann
[12:56:47] Obtained from https://github.com/tseemann/snippy
[12:56:47] Detected operating system: linux
[12:56:47] Enabling bundled linux tools.
[12:56:47] Found bwa - /usr/local/bin/bwa
[12:56:47] Found bcftools - /usr/local/bin/bcftools
[12:56:47] Found samtools - /usr/local/bin/samtools
[12:56:47] Found java - /usr/local/bin/java
[12:56:47] Found snpEff - /usr/local/bin/snpEff
[12:56:47] Found samclip - /usr/local/bin/samclip
[12:56:47] Found seqtk - /usr/local/bin/seqtk
[12:56:47] Found parallel - /usr/local/bin/parallel
[12:56:47] Found freebayes - /usr/local/bin/freebayes
[12:56:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:56:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:56:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:56:47] Found vcfuniq - /usr/local/bin/vcfuniq
[12:56:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:56:47] Found gzip - /bin/gzip
[12:56:47] Found vt - /usr/local/bin/vt
[12:56:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:56:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:56:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:56:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:56:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:56:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:56:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:56:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:57:17] This is snippy 4.6.0Show full stderr[12:57:17] This is snippy 4.6.0
[12:57:17] Written by Torsten Seemann
[12:57:17] Obtained from https://github.com/tseemann/snippy
[12:57:17] Detected operating system: linux
[12:57:17] Enabling bundled linux tools.
[12:57:17] Found bwa - /usr/local/bin/bwa
[12:57:17] Found bcftools - /usr/local/bin/bcftools
[12:57:17] Found samtools - /usr/local/bin/samtools
[12:57:17] Found java - /usr/local/bin/java
[12:57:17] Found snpEff - /usr/local/bin/snpEff
[12:57:17] Found samclip - /usr/local/bin/samclip
[12:57:17] Found seqtk - /usr/local/bin/seqtk
[12:57:17] Found parallel - /usr/local/bin/parallel
[12:57:17] Found freebayes - /usr/local/bin/freebayes
[12:57:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:17] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:17] Found gzip - /bin/gzip
[12:57:17] Found vt - /usr/local/bin/vt
[12:57:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:49:30] This is snippy 4.6.0Show full stderr[12:49:30] This is snippy 4.6.0
[12:49:30] Written by Torsten Seemann
[12:49:30] Obtained from https://github.com/tseemann/snippy
[12:49:30] Detected operating system: linux
[12:49:30] Enabling bundled linux tools.
[12:49:30] Found bwa - /usr/local/bin/bwa
[12:49:30] Found bcftools - /usr/local/bin/bcftools
[12:49:30] Found samtools - /usr/local/bin/samtools
[12:49:30] Found java - /usr/local/bin/java
[12:49:30] Found snpEff - /usr/local/bin/snpEff
[12:49:30] Found samclip - /usr/local/bin/samclip
[12:49:30] Found seqtk - /usr/local/bin/seqtk
[12:49:30] Found parallel - /usr/local/bin/parallel
[12:49:30] Found freebayes - /usr/local/bin/freebayes
[12:49:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:49:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:49:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:49:30] Found vcfuniq - /usr/local/bin/vcfuniq
[12:49:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:49:30] Found gzip - /bin/gzip
[12:49:30] Found vt - /usr/local/bin/vt
[12:49:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:49:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:49:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:49:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:49:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:49:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:49:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:49:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:58:07] This is snippy 4.6.0Show full stderr[12:58:07] This is snippy 4.6.0
[12:58:07] Written by Torsten Seemann
[12:58:07] Obtained from https://github.com/tseemann/snippy
[12:58:07] Detected operating system: linux
[12:58:07] Enabling bundled linux tools.
[12:58:07] Found bwa - /usr/local/bin/bwa
[12:58:07] Found bcftools - /usr/local/bin/bcftools
[12:58:07] Found samtools - /usr/local/bin/samtools
[12:58:07] Found java - /usr/local/bin/java
[12:58:07] Found snpEff - /usr/local/bin/snpEff
[12:58:07] Found samclip - /usr/local/bin/samclip
[12:58:07] Found seqtk - /usr/local/bin/seqtk
[12:58:07] Found parallel - /usr/local/bin/parallel
[12:58:07] Found freebayes - /usr/local/bin/freebayes
[12:58:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:58:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:58:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:58:07] Found vcfuniq - /usr/local/bin/vcfuniq
[12:58:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:58:07] Found gzip - /bin/gzip
[12:58:07] Found vt - /usr/local/bin/vt
[12:58:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:58:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:58:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:58:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:58:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:58:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:58:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:58:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:54:25] This is snippy 4.6.0Show full stderr[12:54:25] This is snippy 4.6.0
[12:54:25] Written by Torsten Seemann
[12:54:25] Obtained from https://github.com/tseemann/snippy
[12:54:25] Detected operating system: linux
[12:54:25] Enabling bundled linux tools.
[12:54:25] Found bwa - /usr/local/bin/bwa
[12:54:25] Found bcftools - /usr/local/bin/bcftools
[12:54:25] Found samtools - /usr/local/bin/samtools
[12:54:25] Found java - /usr/local/bin/java
[12:54:25] Found snpEff - /usr/local/bin/snpEff
[12:54:25] Found samclip - /usr/local/bin/samclip
[12:54:26] Found seqtk - /usr/local/bin/seqtk
[12:54:26] Found parallel - /usr/local/bin/parallel
[12:54:26] Found freebayes - /usr/local/bin/freebayes
[12:54:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:54:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:54:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:54:26] Found vcfuniq - /usr/local/bin/vcfuniq
[12:54:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:54:26] Found gzip - /bin/gzip
[12:54:26] Found vt - /usr/local/bin/vt
[12:54:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:54:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:54:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:54:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:54:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:54:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:54:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:54:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:57:46] This is snippy 4.6.0Show full stderr[12:57:46] This is snippy 4.6.0
[12:57:46] Written by Torsten Seemann
[12:57:46] Obtained from https://github.com/tseemann/snippy
[12:57:46] Detected operating system: linux
[12:57:46] Enabling bundled linux tools.
[12:57:46] Found bwa - /usr/local/bin/bwa
[12:57:46] Found bcftools - /usr/local/bin/bcftools
[12:57:46] Found samtools - /usr/local/bin/samtools
[12:57:46] Found java - /usr/local/bin/java
[12:57:46] Found snpEff - /usr/local/bin/snpEff
[12:57:46] Found samclip - /usr/local/bin/samclip
[12:57:46] Found seqtk - /usr/local/bin/seqtk
[12:57:46] Found parallel - /usr/local/bin/parallel
[12:57:46] Found freebayes - /usr/local/bin/freebayes
[12:57:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:46] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:46] Found gzip - /bin/gzip
[12:57:46] Found vt - /usr/local/bin/vt
[12:57:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:58:17] This is snippy 4.6.0Show full stderr[12:58:17] This is snippy 4.6.0
[12:58:17] Written by Torsten Seemann
[12:58:17] Obtained from https://github.com/tseemann/snippy
[12:58:17] Detected operating system: linux
[12:58:17] Enabling bundled linux tools.
[12:58:17] Found bwa - /usr/local/bin/bwa
[12:58:17] Found bcftools - /usr/local/bin/bcftools
[12:58:17] Found samtools - /usr/local/bin/samtools
[12:58:17] Found java - /usr/local/bin/java
[12:58:17] Found snpEff - /usr/local/bin/snpEff
[12:58:17] Found samclip - /usr/local/bin/samclip
[12:58:17] Found seqtk - /usr/local/bin/seqtk
[12:58:17] Found parallel - /usr/local/bin/parallel
[12:58:17] Found freebayes - /usr/local/bin/freebayes
[12:58:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:58:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:58:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:58:17] Found vcfuniq - /usr/local/bin/vcfuniq
[12:58:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:58:17] Found gzip - /bin/gzip
[12:58:17] Found vt - /usr/local/bin/vt
[12:58:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:58:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:58:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:58:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:58:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:58:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:58:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:58:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:54:35] This is snippy 4.6.0Show full stderr[12:54:35] This is snippy 4.6.0
[12:54:35] Written by Torsten Seemann
[12:54:35] Obtained from https://github.com/tseemann/snippy
[12:54:35] Detected operating system: linux
[12:54:35] Enabling bundled linux tools.
[12:54:35] Found bwa - /usr/local/bin/bwa
[12:54:35] Found bcftools - /usr/local/bin/bcftools
[12:54:35] Found samtools - /usr/local/bin/samtools
[12:54:35] Found java - /usr/local/bin/java
[12:54:35] Found snpEff - /usr/local/bin/snpEff
[12:54:35] Found samclip - /usr/local/bin/samclip
[12:54:35] Found seqtk - /usr/local/bin/seqtk
[12:54:35] Found parallel - /usr/local/bin/parallel
[12:54:35] Found freebayes - /usr/local/bin/freebayes
[12:54:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:54:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:54:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:54:35] Found vcfuniq - /usr/local/bin/vcfuniq
[12:54:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:54:35] Found gzip - /bin/gzip
[12:54:35] Found vt - /usr/local/bin/vt
[12:54:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:54:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:54:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:54:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:54:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:54:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:54:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:54:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:04:03] This is snippy 4.6.0Show full stderr[13:04:03] This is snippy 4.6.0
[13:04:03] Written by Torsten Seemann
[13:04:03] Obtained from https://github.com/tseemann/snippy
[13:04:03] Detected operating system: linux
[13:04:03] Enabling bundled linux tools.
[13:04:03] Found bwa - /usr/local/bin/bwa
[13:04:03] Found bcftools - /usr/local/bin/bcftools
[13:04:03] Found samtools - /usr/local/bin/samtools
[13:04:03] Found java - /usr/local/bin/java
[13:04:03] Found snpEff - /usr/local/bin/snpEff
[13:04:03] Found samclip - /usr/local/bin/samclip
[13:04:03] Found seqtk - /usr/local/bin/seqtk
[13:04:03] Found parallel - /usr/local/bin/parallel
[13:04:03] Found freebayes - /usr/local/bin/freebayes
[13:04:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:04:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:04:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:04:03] Found vcfuniq - /usr/local/bin/vcfuniq
[13:04:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:04:03] Found gzip - /bin/gzip
[13:04:03] Found vt - /usr/local/bin/vt
[13:04:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:04:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:04:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:04:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:04:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:04:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:04:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:04:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:09:47] This is snippy 4.6.0Show full stderr[13:09:47] This is snippy 4.6.0
[13:09:47] Written by Torsten Seemann
[13:09:47] Obtained from https://github.com/tseemann/snippy
[13:09:47] Detected operating system: linux
[13:09:47] Enabling bundled linux tools.
[13:09:47] Found bwa - /usr/local/bin/bwa
[13:09:47] Found bcftools - /usr/local/bin/bcftools
[13:09:47] Found samtools - /usr/local/bin/samtools
[13:09:47] Found java - /usr/local/bin/java
[13:09:47] Found snpEff - /usr/local/bin/snpEff
[13:09:47] Found samclip - /usr/local/bin/samclip
[13:09:47] Found seqtk - /usr/local/bin/seqtk
[13:09:47] Found parallel - /usr/local/bin/parallel
[13:09:47] Found freebayes - /usr/local/bin/freebayes
[13:09:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:09:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:09:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:09:47] Found vcfuniq - /usr/local/bin/vcfuniq
[13:09:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:09:47] Found gzip - /bin/gzip
[13:09:47] Found vt - /usr/local/bin/vt
[13:09:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:09:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:09:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:09:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:09:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:09:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:09:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:09:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:10:49] This is snippy 4.6.0Show full stderr[13:10:49] This is snippy 4.6.0
[13:10:49] Written by Torsten Seemann
[13:10:49] Obtained from https://github.com/tseemann/snippy
[13:10:49] Detected operating system: linux
[13:10:49] Enabling bundled linux tools.
[13:10:49] Found bwa - /usr/local/bin/bwa
[13:10:49] Found bcftools - /usr/local/bin/bcftools
[13:10:49] Found samtools - /usr/local/bin/samtools
[13:10:49] Found java - /usr/local/bin/java
[13:10:49] Found snpEff - /usr/local/bin/snpEff
[13:10:49] Found samclip - /usr/local/bin/samclip
[13:10:49] Found seqtk - /usr/local/bin/seqtk
[13:10:49] Found parallel - /usr/local/bin/parallel
[13:10:49] Found freebayes - /usr/local/bin/freebayes
[13:10:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:10:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:10:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:10:49] Found vcfuniq - /usr/local/bin/vcfuniq
[13:10:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:10:49] Found gzip - /bin/gzip
[13:10:49] Found vt - /usr/local/bin/vt
[13:10:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:10:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:10:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:10:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:10:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:10:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:10:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:10:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:55:19] This is snippy 4.6.0Show full stderr[12:55:19] This is snippy 4.6.0
[12:55:19] Written by Torsten Seemann
[12:55:19] Obtained from https://github.com/tseemann/snippy
[12:55:19] Detected operating system: linux
[12:55:19] Enabling bundled linux tools.
[12:55:19] Found bwa - /usr/local/bin/bwa
[12:55:19] Found bcftools - /usr/local/bin/bcftools
[12:55:19] Found samtools - /usr/local/bin/samtools
[12:55:19] Found java - /usr/local/bin/java
[12:55:20] Found snpEff - /usr/local/bin/snpEff
[12:55:20] Found samclip - /usr/local/bin/samclip
[12:55:20] Found seqtk - /usr/local/bin/seqtk
[12:55:20] Found parallel - /usr/local/bin/parallel
[12:55:20] Found freebayes - /usr/local/bin/freebayes
[12:55:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:55:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:55:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:55:20] Found vcfuniq - /usr/local/bin/vcfuniq
[12:55:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:55:20] Found gzip - /bin/gzip
[12:55:20] Found vt - /usr/local/bin/vt
[12:55:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:55:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:55:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:55:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:55:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:55:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:55:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:55:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:51:03] This is snippy 4.6.0Show full stderr[12:51:03] This is snippy 4.6.0
[12:51:03] Written by Torsten Seemann
[12:51:03] Obtained from https://github.com/tseemann/snippy
[12:51:03] Detected operating system: linux
[12:51:03] Enabling bundled linux tools.
[12:51:03] Found bwa - /usr/local/bin/bwa
[12:51:03] Found bcftools - /usr/local/bin/bcftools
[12:51:03] Found samtools - /usr/local/bin/samtools
[12:51:03] Found java - /usr/local/bin/java
[12:51:03] Found snpEff - /usr/local/bin/snpEff
[12:51:03] Found samclip - /usr/local/bin/samclip
[12:51:03] Found seqtk - /usr/local/bin/seqtk
[12:51:03] Found parallel - /usr/local/bin/parallel
[12:51:03] Found freebayes - /usr/local/bin/freebayes
[12:51:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:51:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:51:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:51:03] Found vcfuniq - /usr/local/bin/vcfuniq
[12:51:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:51:03] Found gzip - /bin/gzip
[12:51:03] Found vt - /usr/local/bin/vt
[12:51:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:51:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:51:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:51:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:51:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:51:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:51:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:51:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:56:41] This is snippy 4.6.0Show full stderr[12:56:41] This is snippy 4.6.0
[12:56:41] Written by Torsten Seemann
[12:56:41] Obtained from https://github.com/tseemann/snippy
[12:56:41] Detected operating system: linux
[12:56:41] Enabling bundled linux tools.
[12:56:41] Found bwa - /usr/local/bin/bwa
[12:56:41] Found bcftools - /usr/local/bin/bcftools
[12:56:41] Found samtools - /usr/local/bin/samtools
[12:56:41] Found java - /usr/local/bin/java
[12:56:41] Found snpEff - /usr/local/bin/snpEff
[12:56:41] Found samclip - /usr/local/bin/samclip
[12:56:41] Found seqtk - /usr/local/bin/seqtk
[12:56:41] Found parallel - /usr/local/bin/parallel
[12:56:41] Found freebayes - /usr/local/bin/freebayes
[12:56:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:56:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:56:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:56:41] Found vcfuniq - /usr/local/bin/vcfuniq
[12:56:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:56:41] Found gzip - /bin/gzip
[12:56:41] Found vt - /usr/local/bin/vt
[12:56:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:56:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:56:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:56:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:56:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:56:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:56:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:56:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:57:42] This is snippy 4.6.0Show full stderr[12:57:42] This is snippy 4.6.0
[12:57:42] Written by Torsten Seemann
[12:57:42] Obtained from https://github.com/tseemann/snippy
[12:57:42] Detected operating system: linux
[12:57:42] Enabling bundled linux tools.
[12:57:42] Found bwa - /usr/local/bin/bwa
[12:57:42] Found bcftools - /usr/local/bin/bcftools
[12:57:42] Found samtools - /usr/local/bin/samtools
[12:57:42] Found java - /usr/local/bin/java
[12:57:42] Found snpEff - /usr/local/bin/snpEff
[12:57:42] Found samclip - /usr/local/bin/samclip
[12:57:42] Found seqtk - /usr/local/bin/seqtk
[12:57:42] Found parallel - /usr/local/bin/parallel
[12:57:42] Found freebayes - /usr/local/bin/freebayes
[12:57:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:42] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:42] Found gzip - /bin/gzip
[12:57:42] Found vt - /usr/local/bin/vt
[12:57:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:56:53] This is snippy 4.6.0Show full stderr[12:56:53] This is snippy 4.6.0
[12:56:53] Written by Torsten Seemann
[12:56:53] Obtained from https://github.com/tseemann/snippy
[12:56:53] Detected operating system: linux
[12:56:53] Enabling bundled linux tools.
[12:56:53] Found bwa - /usr/local/bin/bwa
[12:56:53] Found bcftools - /usr/local/bin/bcftools
[12:56:53] Found samtools - /usr/local/bin/samtools
[12:56:53] Found java - /usr/local/bin/java
[12:56:53] Found snpEff - /usr/local/bin/snpEff
[12:56:53] Found samclip - /usr/local/bin/samclip
[12:56:53] Found seqtk - /usr/local/bin/seqtk
[12:56:53] Found parallel - /usr/local/bin/parallel
[12:56:53] Found freebayes - /usr/local/bin/freebayes
[12:56:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:56:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:56:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:56:53] Found vcfuniq - /usr/local/bin/vcfuniq
[12:56:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:56:53] Found gzip - /bin/gzip
[12:56:53] Found vt - /usr/local/bin/vt
[12:56:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:56:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:56:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:56:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:56:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:56:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:56:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:56:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:57:06] This is snippy 4.6.0Show full stderr[12:57:06] This is snippy 4.6.0
[12:57:06] Written by Torsten Seemann
[12:57:06] Obtained from https://github.com/tseemann/snippy
[12:57:06] Detected operating system: linux
[12:57:06] Enabling bundled linux tools.
[12:57:06] Found bwa - /usr/local/bin/bwa
[12:57:06] Found bcftools - /usr/local/bin/bcftools
[12:57:06] Found samtools - /usr/local/bin/samtools
[12:57:06] Found java - /usr/local/bin/java
[12:57:06] Found snpEff - /usr/local/bin/snpEff
[12:57:06] Found samclip - /usr/local/bin/samclip
[12:57:06] Found seqtk - /usr/local/bin/seqtk
[12:57:06] Found parallel - /usr/local/bin/parallel
[12:57:06] Found freebayes - /usr/local/bin/freebayes
[12:57:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:06] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:06] Found gzip - /bin/gzip
[12:57:06] Found vt - /usr/local/bin/vt
[12:57:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:58:15] This is snippy 4.6.0Show full stderr[12:58:15] This is snippy 4.6.0
[12:58:15] Written by Torsten Seemann
[12:58:15] Obtained from https://github.com/tseemann/snippy
[12:58:15] Detected operating system: linux
[12:58:15] Enabling bundled linux tools.
[12:58:15] Found bwa - /usr/local/bin/bwa
[12:58:15] Found bcftools - /usr/local/bin/bcftools
[12:58:15] Found samtools - /usr/local/bin/samtools
[12:58:15] Found java - /usr/local/bin/java
[12:58:15] Found snpEff - /usr/local/bin/snpEff
[12:58:15] Found samclip - /usr/local/bin/samclip
[12:58:15] Found seqtk - /usr/local/bin/seqtk
[12:58:15] Found parallel - /usr/local/bin/parallel
[12:58:15] Found freebayes - /usr/local/bin/freebayes
[12:58:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:58:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:58:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:58:15] Found vcfuniq - /usr/local/bin/vcfuniq
[12:58:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:58:15] Found gzip - /bin/gzip
[12:58:15] Found vt - /usr/local/bin/vt
[12:58:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:58:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:58:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:58:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:58:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:58:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:58:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:58:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:58:03] This is snippy 4.6.0Show full stderr[12:58:03] This is snippy 4.6.0
[12:58:03] Written by Torsten Seemann
[12:58:03] Obtained from https://github.com/tseemann/snippy
[12:58:03] Detected operating system: linux
[12:58:03] Enabling bundled linux tools.
[12:58:03] Found bwa - /usr/local/bin/bwa
[12:58:03] Found bcftools - /usr/local/bin/bcftools
[12:58:03] Found samtools - /usr/local/bin/samtools
[12:58:03] Found java - /usr/local/bin/java
[12:58:03] Found snpEff - /usr/local/bin/snpEff
[12:58:03] Found samclip - /usr/local/bin/samclip
[12:58:03] Found seqtk - /usr/local/bin/seqtk
[12:58:03] Found parallel - /usr/local/bin/parallel
[12:58:03] Found freebayes - /usr/local/bin/freebayes
[12:58:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:58:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:58:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:58:03] Found vcfuniq - /usr/local/bin/vcfuniq
[12:58:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:58:03] Found gzip - /bin/gzip
[12:58:03] Found vt - /usr/local/bin/vt
[12:58:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:58:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:58:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:58:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:58:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:58:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:58:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:58:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:48:58] This is snippy 4.6.0Show full stderr[12:48:58] This is snippy 4.6.0
[12:48:58] Written by Torsten Seemann
[12:48:58] Obtained from https://github.com/tseemann/snippy
[12:48:58] Detected operating system: linux
[12:48:58] Enabling bundled linux tools.
[12:48:58] Found bwa - /usr/local/bin/bwa
[12:48:58] Found bcftools - /usr/local/bin/bcftools
[12:48:58] Found samtools - /usr/local/bin/samtools
[12:48:58] Found java - /usr/local/bin/java
[12:48:58] Found snpEff - /usr/local/bin/snpEff
[12:48:58] Found samclip - /usr/local/bin/samclip
[12:48:58] Found seqtk - /usr/local/bin/seqtk
[12:48:58] Found parallel - /usr/local/bin/parallel
[12:48:58] Found freebayes - /usr/local/bin/freebayes
[12:48:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:48:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:48:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:48:58] Found vcfuniq - /usr/local/bin/vcfuniq
[12:48:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:48:58] Found gzip - /bin/gzip
[12:48:58] Found vt - /usr/local/bin/vt
[12:48:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:48:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:48:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:48:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:48:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:48:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:48:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:48:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:23:55] This is snippy 4.6.0Show full stderr[13:23:55] This is snippy 4.6.0
[13:23:55] Written by Torsten Seemann
[13:23:55] Obtained from https://github.com/tseemann/snippy
[13:23:55] Detected operating system: linux
[13:23:55] Enabling bundled linux tools.
[13:23:55] Found bwa - /usr/local/bin/bwa
[13:23:55] Found bcftools - /usr/local/bin/bcftools
[13:23:55] Found samtools - /usr/local/bin/samtools
[13:23:55] Found java - /usr/local/bin/java
[13:23:55] Found snpEff - /usr/local/bin/snpEff
[13:23:55] Found samclip - /usr/local/bin/samclip
[13:23:55] Found seqtk - /usr/local/bin/seqtk
[13:23:55] Found parallel - /usr/local/bin/parallel
[13:23:55] Found freebayes - /usr/local/bin/freebayes
[13:23:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:23:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:23:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:23:55] Found vcfuniq - /usr/local/bin/vcfuniq
[13:23:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:23:55] Found gzip - /bin/gzip
[13:23:55] Found vt - /usr/local/bin/vt
[13:23:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:23:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:23:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:23:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:23:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:24:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:24:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:24:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:17:51] This is snippy 4.6.0Show full stderr[13:17:51] This is snippy 4.6.0
[13:17:51] Written by Torsten Seemann
[13:17:51] Obtained from https://github.com/tseemann/snippy
[13:17:51] Detected operating system: linux
[13:17:51] Enabling bundled linux tools.
[13:17:51] Found bwa - /usr/local/bin/bwa
[13:17:51] Found bcftools - /usr/local/bin/bcftools
[13:17:51] Found samtools - /usr/local/bin/samtools
[13:17:51] Found java - /usr/local/bin/java
[13:17:51] Found snpEff - /usr/local/bin/snpEff
[13:17:51] Found samclip - /usr/local/bin/samclip
[13:17:51] Found seqtk - /usr/local/bin/seqtk
[13:17:51] Found parallel - /usr/local/bin/parallel
[13:17:51] Found freebayes - /usr/local/bin/freebayes
[13:17:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:17:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:17:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:17:51] Found vcfuniq - /usr/local/bin/vcfuniq
[13:17:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:17:51] Found gzip - /bin/gzip
[13:17:51] Found vt - /usr/local/bin/vt
[13:17:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:17:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:17:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:17:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:17:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:17:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:17:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:17:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:24:07] This is snippy 4.6.0Show full stderr[13:24:07] This is snippy 4.6.0
[13:24:07] Written by Torsten Seemann
[13:24:07] Obtained from https://github.com/tseemann/snippy
[13:24:07] Detected operating system: linux
[13:24:07] Enabling bundled linux tools.
[13:24:07] Found bwa - /usr/local/bin/bwa
[13:24:07] Found bcftools - /usr/local/bin/bcftools
[13:24:07] Found samtools - /usr/local/bin/samtools
[13:24:07] Found java - /usr/local/bin/java
[13:24:07] Found snpEff - /usr/local/bin/snpEff
[13:24:07] Found samclip - /usr/local/bin/samclip
[13:24:07] Found seqtk - /usr/local/bin/seqtk
[13:24:07] Found parallel - /usr/local/bin/parallel
[13:24:07] Found freebayes - /usr/local/bin/freebayes
[13:24:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:24:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:24:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:24:07] Found vcfuniq - /usr/local/bin/vcfuniq
[13:24:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:24:07] Found gzip - /bin/gzip
[13:24:07] Found vt - /usr/local/bin/vt
[13:24:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:24:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:24:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:24:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:24:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:24:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:24:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:24:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:51:42] This is snippy 4.6.0Show full stderr[12:51:42] This is snippy 4.6.0
[12:51:42] Written by Torsten Seemann
[12:51:42] Obtained from https://github.com/tseemann/snippy
[12:51:42] Detected operating system: linux
[12:51:42] Enabling bundled linux tools.
[12:51:42] Found bwa - /usr/local/bin/bwa
[12:51:42] Found bcftools - /usr/local/bin/bcftools
[12:51:42] Found samtools - /usr/local/bin/samtools
[12:51:42] Found java - /usr/local/bin/java
[12:51:42] Found snpEff - /usr/local/bin/snpEff
[12:51:42] Found samclip - /usr/local/bin/samclip
[12:51:42] Found seqtk - /usr/local/bin/seqtk
[12:51:42] Found parallel - /usr/local/bin/parallel
[12:51:42] Found freebayes - /usr/local/bin/freebayes
[12:51:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:51:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:51:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:51:42] Found vcfuniq - /usr/local/bin/vcfuniq
[12:51:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:51:42] Found gzip - /bin/gzip
[12:51:42] Found vt - /usr/local/bin/vt
[12:51:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:51:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:51:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:51:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:51:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:51:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:51:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:51:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:57:37] This is snippy 4.6.0Show full stderr[12:57:37] This is snippy 4.6.0
[12:57:37] Written by Torsten Seemann
[12:57:37] Obtained from https://github.com/tseemann/snippy
[12:57:37] Detected operating system: linux
[12:57:37] Enabling bundled linux tools.
[12:57:37] Found bwa - /usr/local/bin/bwa
[12:57:37] Found bcftools - /usr/local/bin/bcftools
[12:57:37] Found samtools - /usr/local/bin/samtools
[12:57:37] Found java - /usr/local/bin/java
[12:57:37] Found snpEff - /usr/local/bin/snpEff
[12:57:37] Found samclip - /usr/local/bin/samclip
[12:57:37] Found seqtk - /usr/local/bin/seqtk
[12:57:37] Found parallel - /usr/local/bin/parallel
[12:57:37] Found freebayes - /usr/local/bin/freebayes
[12:57:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:37] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:37] Found gzip - /bin/gzip
[12:57:37] Found vt - /usr/local/bin/vt
[12:57:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:57:54] This is snippy 4.6.0Show full stderr[12:57:54] This is snippy 4.6.0
[12:57:54] Written by Torsten Seemann
[12:57:54] Obtained from https://github.com/tseemann/snippy
[12:57:54] Detected operating system: linux
[12:57:54] Enabling bundled linux tools.
[12:57:54] Found bwa - /usr/local/bin/bwa
[12:57:54] Found bcftools - /usr/local/bin/bcftools
[12:57:54] Found samtools - /usr/local/bin/samtools
[12:57:54] Found java - /usr/local/bin/java
[12:57:54] Found snpEff - /usr/local/bin/snpEff
[12:57:54] Found samclip - /usr/local/bin/samclip
[12:57:54] Found seqtk - /usr/local/bin/seqtk
[12:57:54] Found parallel - /usr/local/bin/parallel
[12:57:54] Found freebayes - /usr/local/bin/freebayes
[12:57:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:54] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:55] Found gzip - /bin/gzip
[12:57:55] Found vt - /usr/local/bin/vt
[12:57:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:03:54] This is snippy 4.6.0Show full stderr[13:03:54] This is snippy 4.6.0
[13:03:54] Written by Torsten Seemann
[13:03:54] Obtained from https://github.com/tseemann/snippy
[13:03:54] Detected operating system: linux
[13:03:54] Enabling bundled linux tools.
[13:03:54] Found bwa - /usr/local/bin/bwa
[13:03:54] Found bcftools - /usr/local/bin/bcftools
[13:03:54] Found samtools - /usr/local/bin/samtools
[13:03:54] Found java - /usr/local/bin/java
[13:03:54] Found snpEff - /usr/local/bin/snpEff
[13:03:54] Found samclip - /usr/local/bin/samclip
[13:03:54] Found seqtk - /usr/local/bin/seqtk
[13:03:54] Found parallel - /usr/local/bin/parallel
[13:03:54] Found freebayes - /usr/local/bin/freebayes
[13:03:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:03:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:03:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:03:54] Found vcfuniq - /usr/local/bin/vcfuniq
[13:03:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:03:54] Found gzip - /bin/gzip
[13:03:54] Found vt - /usr/local/bin/vt
[13:03:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:03:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:03:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:03:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:03:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:03:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:03:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:03:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:51:18] This is snippy 4.6.0Show full stderr[12:51:18] This is snippy 4.6.0
[12:51:18] Written by Torsten Seemann
[12:51:18] Obtained from https://github.com/tseemann/snippy
[12:51:18] Detected operating system: linux
[12:51:18] Enabling bundled linux tools.
[12:51:18] Found bwa - /usr/local/bin/bwa
[12:51:18] Found bcftools - /usr/local/bin/bcftools
[12:51:18] Found samtools - /usr/local/bin/samtools
[12:51:18] Found java - /usr/local/bin/java
[12:51:18] Found snpEff - /usr/local/bin/snpEff
[12:51:18] Found samclip - /usr/local/bin/samclip
[12:51:18] Found seqtk - /usr/local/bin/seqtk
[12:51:18] Found parallel - /usr/local/bin/parallel
[12:51:18] Found freebayes - /usr/local/bin/freebayes
[12:51:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:51:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:51:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:51:18] Found vcfuniq - /usr/local/bin/vcfuniq
[12:51:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:51:18] Found gzip - /bin/gzip
[12:51:18] Found vt - /usr/local/bin/vt
[12:51:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:51:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:51:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:51:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:51:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:51:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:51:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:51:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:55:36] This is snippy 4.6.0Show full stderr[12:55:36] This is snippy 4.6.0
[12:55:36] Written by Torsten Seemann
[12:55:36] Obtained from https://github.com/tseemann/snippy
[12:55:36] Detected operating system: linux
[12:55:36] Enabling bundled linux tools.
[12:55:36] Found bwa - /usr/local/bin/bwa
[12:55:36] Found bcftools - /usr/local/bin/bcftools
[12:55:36] Found samtools - /usr/local/bin/samtools
[12:55:36] Found java - /usr/local/bin/java
[12:55:36] Found snpEff - /usr/local/bin/snpEff
[12:55:36] Found samclip - /usr/local/bin/samclip
[12:55:36] Found seqtk - /usr/local/bin/seqtk
[12:55:36] Found parallel - /usr/local/bin/parallel
[12:55:36] Found freebayes - /usr/local/bin/freebayes
[12:55:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:55:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:55:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:55:36] Found vcfuniq - /usr/local/bin/vcfuniq
[12:55:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:55:36] Found gzip - /bin/gzip
[12:55:36] Found vt - /usr/local/bin/vt
[12:55:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:55:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:55:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:55:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:55:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:55:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:55:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:55:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:55:47] This is snippy 4.6.0Show full stderr[12:55:47] This is snippy 4.6.0
[12:55:47] Written by Torsten Seemann
[12:55:47] Obtained from https://github.com/tseemann/snippy
[12:55:47] Detected operating system: linux
[12:55:47] Enabling bundled linux tools.
[12:55:47] Found bwa - /usr/local/bin/bwa
[12:55:47] Found bcftools - /usr/local/bin/bcftools
[12:55:47] Found samtools - /usr/local/bin/samtools
[12:55:47] Found java - /usr/local/bin/java
[12:55:48] Found snpEff - /usr/local/bin/snpEff
[12:55:48] Found samclip - /usr/local/bin/samclip
[12:55:48] Found seqtk - /usr/local/bin/seqtk
[12:55:48] Found parallel - /usr/local/bin/parallel
[12:55:48] Found freebayes - /usr/local/bin/freebayes
[12:55:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:55:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:55:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:55:48] Found vcfuniq - /usr/local/bin/vcfuniq
[12:55:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:55:48] Found gzip - /bin/gzip
[12:55:48] Found vt - /usr/local/bin/vt
[12:55:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:55:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:55:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:55:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:55:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:55:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:55:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:55:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:04:22] This is snippy 4.6.0Show full stderr[13:04:22] This is snippy 4.6.0
[13:04:22] Written by Torsten Seemann
[13:04:22] Obtained from https://github.com/tseemann/snippy
[13:04:22] Detected operating system: linux
[13:04:22] Enabling bundled linux tools.
[13:04:22] Found bwa - /usr/local/bin/bwa
[13:04:22] Found bcftools - /usr/local/bin/bcftools
[13:04:22] Found samtools - /usr/local/bin/samtools
[13:04:22] Found java - /usr/local/bin/java
[13:04:22] Found snpEff - /usr/local/bin/snpEff
[13:04:22] Found samclip - /usr/local/bin/samclip
[13:04:22] Found seqtk - /usr/local/bin/seqtk
[13:04:22] Found parallel - /usr/local/bin/parallel
[13:04:22] Found freebayes - /usr/local/bin/freebayes
[13:04:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:04:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:04:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:04:22] Found vcfuniq - /usr/local/bin/vcfuniq
[13:04:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:04:22] Found gzip - /bin/gzip
[13:04:22] Found vt - /usr/local/bin/vt
[13:04:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:04:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:04:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:04:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:04:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:04:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:04:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:04:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:10:08] This is snippy 4.6.0Show full stderr[13:10:08] This is snippy 4.6.0
[13:10:08] Written by Torsten Seemann
[13:10:08] Obtained from https://github.com/tseemann/snippy
[13:10:08] Detected operating system: linux
[13:10:08] Enabling bundled linux tools.
[13:10:08] Found bwa - /usr/local/bin/bwa
[13:10:08] Found bcftools - /usr/local/bin/bcftools
[13:10:08] Found samtools - /usr/local/bin/samtools
[13:10:08] Found java - /usr/local/bin/java
[13:10:08] Found snpEff - /usr/local/bin/snpEff
[13:10:08] Found samclip - /usr/local/bin/samclip
[13:10:08] Found seqtk - /usr/local/bin/seqtk
[13:10:08] Found parallel - /usr/local/bin/parallel
[13:10:08] Found freebayes - /usr/local/bin/freebayes
[13:10:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:10:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:10:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:10:08] Found vcfuniq - /usr/local/bin/vcfuniq
[13:10:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:10:08] Found gzip - /bin/gzip
[13:10:08] Found vt - /usr/local/bin/vt
[13:10:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:10:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:10:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:10:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:10:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:10:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:10:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:10:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:16:56] This is snippy 4.6.0Show full stderr[13:16:56] This is snippy 4.6.0
[13:16:56] Written by Torsten Seemann
[13:16:56] Obtained from https://github.com/tseemann/snippy
[13:16:56] Detected operating system: linux
[13:16:56] Enabling bundled linux tools.
[13:16:56] Found bwa - /usr/local/bin/bwa
[13:16:56] Found bcftools - /usr/local/bin/bcftools
[13:16:56] Found samtools - /usr/local/bin/samtools
[13:16:56] Found java - /usr/local/bin/java
[13:16:56] Found snpEff - /usr/local/bin/snpEff
[13:16:56] Found samclip - /usr/local/bin/samclip
[13:16:56] Found seqtk - /usr/local/bin/seqtk
[13:16:56] Found parallel - /usr/local/bin/parallel
[13:16:56] Found freebayes - /usr/local/bin/freebayes
[13:16:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:16:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:16:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:16:56] Found vcfuniq - /usr/local/bin/vcfuniq
[13:16:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:16:56] Found gzip - /bin/gzip
[13:16:56] Found vt - /usr/local/bin/vt
[13:16:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:16:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:16:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:16:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:16:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:16:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:16:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:16:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:16:47] This is snippy 4.6.0Show full stderr[13:16:47] This is snippy 4.6.0
[13:16:47] Written by Torsten Seemann
[13:16:47] Obtained from https://github.com/tseemann/snippy
[13:16:47] Detected operating system: linux
[13:16:47] Enabling bundled linux tools.
[13:16:47] Found bwa - /usr/local/bin/bwa
[13:16:47] Found bcftools - /usr/local/bin/bcftools
[13:16:47] Found samtools - /usr/local/bin/samtools
[13:16:47] Found java - /usr/local/bin/java
[13:16:47] Found snpEff - /usr/local/bin/snpEff
[13:16:47] Found samclip - /usr/local/bin/samclip
[13:16:47] Found seqtk - /usr/local/bin/seqtk
[13:16:47] Found parallel - /usr/local/bin/parallel
[13:16:47] Found freebayes - /usr/local/bin/freebayes
[13:16:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:16:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:16:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:16:47] Found vcfuniq - /usr/local/bin/vcfuniq
[13:16:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:16:47] Found gzip - /bin/gzip
[13:16:47] Found vt - /usr/local/bin/vt
[13:16:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:16:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:16:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:16:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:16:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:16:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:16:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:16:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:25:32] This is snippy 4.6.0Show full stderr[13:25:32] This is snippy 4.6.0
[13:25:32] Written by Torsten Seemann
[13:25:32] Obtained from https://github.com/tseemann/snippy
[13:25:32] Detected operating system: linux
[13:25:32] Enabling bundled linux tools.
[13:25:32] Found bwa - /usr/local/bin/bwa
[13:25:32] Found bcftools - /usr/local/bin/bcftools
[13:25:32] Found samtools - /usr/local/bin/samtools
[13:25:32] Found java - /usr/local/bin/java
[13:25:32] Found snpEff - /usr/local/bin/snpEff
[13:25:32] Found samclip - /usr/local/bin/samclip
[13:25:32] Found seqtk - /usr/local/bin/seqtk
[13:25:32] Found parallel - /usr/local/bin/parallel
[13:25:32] Found freebayes - /usr/local/bin/freebayes
[13:25:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:25:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:25:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:25:32] Found vcfuniq - /usr/local/bin/vcfuniq
[13:25:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:25:32] Found gzip - /bin/gzip
[13:25:32] Found vt - /usr/local/bin/vt
[13:25:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:25:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:25:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:25:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:25:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:25:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:25:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:25:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:56:05] This is snippy 4.6.0Show full stderr[12:56:05] This is snippy 4.6.0
[12:56:05] Written by Torsten Seemann
[12:56:05] Obtained from https://github.com/tseemann/snippy
[12:56:05] Detected operating system: linux
[12:56:05] Enabling bundled linux tools.
[12:56:05] Found bwa - /usr/local/bin/bwa
[12:56:05] Found bcftools - /usr/local/bin/bcftools
[12:56:05] Found samtools - /usr/local/bin/samtools
[12:56:05] Found java - /usr/local/bin/java
[12:56:05] Found snpEff - /usr/local/bin/snpEff
[12:56:05] Found samclip - /usr/local/bin/samclip
[12:56:05] Found seqtk - /usr/local/bin/seqtk
[12:56:05] Found parallel - /usr/local/bin/parallel
[12:56:05] Found freebayes - /usr/local/bin/freebayes
[12:56:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:56:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:56:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:56:05] Found vcfuniq - /usr/local/bin/vcfuniq
[12:56:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:56:05] Found gzip - /bin/gzip
[12:56:05] Found vt - /usr/local/bin/vt
[12:56:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:56:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:56:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:56:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:56:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:56:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:56:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:56:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:56:14] This is snippy 4.6.0Show full stderr[12:56:14] This is snippy 4.6.0
[12:56:14] Written by Torsten Seemann
[12:56:14] Obtained from https://github.com/tseemann/snippy
[12:56:14] Detected operating system: linux
[12:56:14] Enabling bundled linux tools.
[12:56:14] Found bwa - /usr/local/bin/bwa
[12:56:14] Found bcftools - /usr/local/bin/bcftools
[12:56:14] Found samtools - /usr/local/bin/samtools
[12:56:14] Found java - /usr/local/bin/java
[12:56:14] Found snpEff - /usr/local/bin/snpEff
[12:56:14] Found samclip - /usr/local/bin/samclip
[12:56:14] Found seqtk - /usr/local/bin/seqtk
[12:56:14] Found parallel - /usr/local/bin/parallel
[12:56:14] Found freebayes - /usr/local/bin/freebayes
[12:56:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:56:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:56:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:56:14] Found vcfuniq - /usr/local/bin/vcfuniq
[12:56:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:56:14] Found gzip - /bin/gzip
[12:56:14] Found vt - /usr/local/bin/vt
[12:56:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:56:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:56:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:56:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:56:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:56:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:56:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:56:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:25:49] This is snippy 4.6.0Show full stderr[13:25:49] This is snippy 4.6.0
[13:25:49] Written by Torsten Seemann
[13:25:49] Obtained from https://github.com/tseemann/snippy
[13:25:49] Detected operating system: linux
[13:25:49] Enabling bundled linux tools.
[13:25:49] Found bwa - /usr/local/bin/bwa
[13:25:49] Found bcftools - /usr/local/bin/bcftools
[13:25:49] Found samtools - /usr/local/bin/samtools
[13:25:49] Found java - /usr/local/bin/java
[13:25:49] Found snpEff - /usr/local/bin/snpEff
[13:25:49] Found samclip - /usr/local/bin/samclip
[13:25:49] Found seqtk - /usr/local/bin/seqtk
[13:25:49] Found parallel - /usr/local/bin/parallel
[13:25:49] Found freebayes - /usr/local/bin/freebayes
[13:25:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:25:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:25:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:25:49] Found vcfuniq - /usr/local/bin/vcfuniq
[13:25:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:25:49] Found gzip - /bin/gzip
[13:25:49] Found vt - /usr/local/bin/vt
[13:25:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:25:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:25:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:25:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:25:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:25:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:25:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:25:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:56:11] This is snippy 4.6.0Show full stderr[12:56:11] This is snippy 4.6.0
[12:56:11] Written by Torsten Seemann
[12:56:11] Obtained from https://github.com/tseemann/snippy
[12:56:11] Detected operating system: linux
[12:56:11] Enabling bundled linux tools.
[12:56:11] Found bwa - /usr/local/bin/bwa
[12:56:11] Found bcftools - /usr/local/bin/bcftools
[12:56:11] Found samtools - /usr/local/bin/samtools
[12:56:11] Found java - /usr/local/bin/java
[12:56:11] Found snpEff - /usr/local/bin/snpEff
[12:56:11] Found samclip - /usr/local/bin/samclip
[12:56:11] Found seqtk - /usr/local/bin/seqtk
[12:56:11] Found parallel - /usr/local/bin/parallel
[12:56:11] Found freebayes - /usr/local/bin/freebayes
[12:56:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:56:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:56:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:56:11] Found vcfuniq - /usr/local/bin/vcfuniq
[12:56:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:56:11] Found gzip - /bin/gzip
[12:56:11] Found vt - /usr/local/bin/vt
[12:56:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:56:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:56:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:56:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:56:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:56:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:56:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:56:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:56:17] This is snippy 4.6.0Show full stderr[12:56:17] This is snippy 4.6.0
[12:56:17] Written by Torsten Seemann
[12:56:17] Obtained from https://github.com/tseemann/snippy
[12:56:17] Detected operating system: linux
[12:56:17] Enabling bundled linux tools.
[12:56:17] Found bwa - /usr/local/bin/bwa
[12:56:17] Found bcftools - /usr/local/bin/bcftools
[12:56:17] Found samtools - /usr/local/bin/samtools
[12:56:17] Found java - /usr/local/bin/java
[12:56:17] Found snpEff - /usr/local/bin/snpEff
[12:56:17] Found samclip - /usr/local/bin/samclip
[12:56:17] Found seqtk - /usr/local/bin/seqtk
[12:56:17] Found parallel - /usr/local/bin/parallel
[12:56:17] Found freebayes - /usr/local/bin/freebayes
[12:56:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:56:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:56:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:56:17] Found vcfuniq - /usr/local/bin/vcfuniq
[12:56:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:56:17] Found gzip - /bin/gzip
[12:56:17] Found vt - /usr/local/bin/vt
[12:56:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:56:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:56:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:56:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:56:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:56:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:56:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:56:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:56:35] This is snippy 4.6.0Show full stderr[12:56:35] This is snippy 4.6.0
[12:56:35] Written by Torsten Seemann
[12:56:35] Obtained from https://github.com/tseemann/snippy
[12:56:35] Detected operating system: linux
[12:56:35] Enabling bundled linux tools.
[12:56:35] Found bwa - /usr/local/bin/bwa
[12:56:35] Found bcftools - /usr/local/bin/bcftools
[12:56:35] Found samtools - /usr/local/bin/samtools
[12:56:35] Found java - /usr/local/bin/java
[12:56:35] Found snpEff - /usr/local/bin/snpEff
[12:56:35] Found samclip - /usr/local/bin/samclip
[12:56:35] Found seqtk - /usr/local/bin/seqtk
[12:56:35] Found parallel - /usr/local/bin/parallel
[12:56:35] Found freebayes - /usr/local/bin/freebayes
[12:56:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:56:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:56:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:56:35] Found vcfuniq - /usr/local/bin/vcfuniq
[12:56:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:56:35] Found gzip - /bin/gzip
[12:56:35] Found vt - /usr/local/bin/vt
[12:56:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:56:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:56:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:56:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:56:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:56:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:56:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:56:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:24:32] This is snippy 4.6.0Show full stderr[13:24:32] This is snippy 4.6.0
[13:24:32] Written by Torsten Seemann
[13:24:32] Obtained from https://github.com/tseemann/snippy
[13:24:32] Detected operating system: linux
[13:24:32] Enabling bundled linux tools.
[13:24:32] Found bwa - /usr/local/bin/bwa
[13:24:32] Found bcftools - /usr/local/bin/bcftools
[13:24:32] Found samtools - /usr/local/bin/samtools
[13:24:32] Found java - /usr/local/bin/java
[13:24:32] Found snpEff - /usr/local/bin/snpEff
[13:24:32] Found samclip - /usr/local/bin/samclip
[13:24:32] Found seqtk - /usr/local/bin/seqtk
[13:24:32] Found parallel - /usr/local/bin/parallel
[13:24:32] Found freebayes - /usr/local/bin/freebayes
[13:24:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:24:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:24:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:24:32] Found vcfuniq - /usr/local/bin/vcfuniq
[13:24:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:24:32] Found gzip - /bin/gzip
[13:24:32] Found vt - /usr/local/bin/vt
[13:24:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:24:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:24:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:24:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:24:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:24:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:24:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:24:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:30:25] This is snippy 4.6.0Show full stderr[13:30:25] This is snippy 4.6.0
[13:30:25] Written by Torsten Seemann
[13:30:25] Obtained from https://github.com/tseemann/snippy
[13:30:25] Detected operating system: linux
[13:30:25] Enabling bundled linux tools.
[13:30:25] Found bwa - /usr/local/bin/bwa
[13:30:25] Found bcftools - /usr/local/bin/bcftools
[13:30:25] Found samtools - /usr/local/bin/samtools
[13:30:25] Found java - /usr/local/bin/java
[13:30:25] Found snpEff - /usr/local/bin/snpEff
[13:30:25] Found samclip - /usr/local/bin/samclip
[13:30:25] Found seqtk - /usr/local/bin/seqtk
[13:30:25] Found parallel - /usr/local/bin/parallel
[13:30:25] Found freebayes - /usr/local/bin/freebayes
[13:30:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:30:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:30:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:30:26] Found vcfuniq - /usr/local/bin/vcfuniq
[13:30:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:30:26] Found gzip - /bin/gzip
[13:30:26] Found vt - /usr/local/bin/vt
[13:30:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:30:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:30:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:30:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:30:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:30:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:30:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:30:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:56:38] This is snippy 4.6.0Show full stderr[12:56:38] This is snippy 4.6.0
[12:56:38] Written by Torsten Seemann
[12:56:38] Obtained from https://github.com/tseemann/snippy
[12:56:38] Detected operating system: linux
[12:56:38] Enabling bundled linux tools.
[12:56:38] Found bwa - /usr/local/bin/bwa
[12:56:38] Found bcftools - /usr/local/bin/bcftools
[12:56:38] Found samtools - /usr/local/bin/samtools
[12:56:38] Found java - /usr/local/bin/java
[12:56:38] Found snpEff - /usr/local/bin/snpEff
[12:56:38] Found samclip - /usr/local/bin/samclip
[12:56:38] Found seqtk - /usr/local/bin/seqtk
[12:56:38] Found parallel - /usr/local/bin/parallel
[12:56:38] Found freebayes - /usr/local/bin/freebayes
[12:56:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:56:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:56:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:56:38] Found vcfuniq - /usr/local/bin/vcfuniq
[12:56:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:56:38] Found gzip - /bin/gzip
[12:56:38] Found vt - /usr/local/bin/vt
[12:56:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:56:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:56:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:56:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:56:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:56:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:56:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:56:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:56:50] This is snippy 4.6.0Show full stderr[12:56:50] This is snippy 4.6.0
[12:56:50] Written by Torsten Seemann
[12:56:50] Obtained from https://github.com/tseemann/snippy
[12:56:50] Detected operating system: linux
[12:56:50] Enabling bundled linux tools.
[12:56:50] Found bwa - /usr/local/bin/bwa
[12:56:50] Found bcftools - /usr/local/bin/bcftools
[12:56:50] Found samtools - /usr/local/bin/samtools
[12:56:50] Found java - /usr/local/bin/java
[12:56:50] Found snpEff - /usr/local/bin/snpEff
[12:56:50] Found samclip - /usr/local/bin/samclip
[12:56:50] Found seqtk - /usr/local/bin/seqtk
[12:56:50] Found parallel - /usr/local/bin/parallel
[12:56:50] Found freebayes - /usr/local/bin/freebayes
[12:56:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:56:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:56:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:56:50] Found vcfuniq - /usr/local/bin/vcfuniq
[12:56:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:56:50] Found gzip - /bin/gzip
[12:56:50] Found vt - /usr/local/bin/vt
[12:56:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:56:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:56:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:56:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:56:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:56:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:56:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:56:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:32:09] This is snippy 4.6.0Show full stderr[13:32:09] This is snippy 4.6.0
[13:32:09] Written by Torsten Seemann
[13:32:09] Obtained from https://github.com/tseemann/snippy
[13:32:09] Detected operating system: linux
[13:32:09] Enabling bundled linux tools.
[13:32:09] Found bwa - /usr/local/bin/bwa
[13:32:09] Found bcftools - /usr/local/bin/bcftools
[13:32:09] Found samtools - /usr/local/bin/samtools
[13:32:09] Found java - /usr/local/bin/java
[13:32:09] Found snpEff - /usr/local/bin/snpEff
[13:32:09] Found samclip - /usr/local/bin/samclip
[13:32:09] Found seqtk - /usr/local/bin/seqtk
[13:32:09] Found parallel - /usr/local/bin/parallel
[13:32:09] Found freebayes - /usr/local/bin/freebayes
[13:32:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:32:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:32:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:32:09] Found vcfuniq - /usr/local/bin/vcfuniq
[13:32:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:32:09] Found gzip - /bin/gzip
[13:32:09] Found vt - /usr/local/bin/vt
[13:32:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:32:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:32:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:32:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:32:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:32:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:32:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:32:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:56:56] This is snippy 4.6.0Show full stderr[12:56:56] This is snippy 4.6.0
[12:56:56] Written by Torsten Seemann
[12:56:56] Obtained from https://github.com/tseemann/snippy
[12:56:56] Detected operating system: linux
[12:56:56] Enabling bundled linux tools.
[12:56:56] Found bwa - /usr/local/bin/bwa
[12:56:56] Found bcftools - /usr/local/bin/bcftools
[12:56:56] Found samtools - /usr/local/bin/samtools
[12:56:56] Found java - /usr/local/bin/java
[12:56:56] Found snpEff - /usr/local/bin/snpEff
[12:56:56] Found samclip - /usr/local/bin/samclip
[12:56:56] Found seqtk - /usr/local/bin/seqtk
[12:56:56] Found parallel - /usr/local/bin/parallel
[12:56:56] Found freebayes - /usr/local/bin/freebayes
[12:56:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:56:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:56:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:56:56] Found vcfuniq - /usr/local/bin/vcfuniq
[12:56:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:56:56] Found gzip - /bin/gzip
[12:56:56] Found vt - /usr/local/bin/vt
[12:56:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:56:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:56:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:56:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:56:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:56:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:56:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:56:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:57:23] This is snippy 4.6.0Show full stderr[12:57:23] This is snippy 4.6.0
[12:57:23] Written by Torsten Seemann
[12:57:23] Obtained from https://github.com/tseemann/snippy
[12:57:23] Detected operating system: linux
[12:57:23] Enabling bundled linux tools.
[12:57:23] Found bwa - /usr/local/bin/bwa
[12:57:23] Found bcftools - /usr/local/bin/bcftools
[12:57:23] Found samtools - /usr/local/bin/samtools
[12:57:23] Found java - /usr/local/bin/java
[12:57:23] Found snpEff - /usr/local/bin/snpEff
[12:57:23] Found samclip - /usr/local/bin/samclip
[12:57:23] Found seqtk - /usr/local/bin/seqtk
[12:57:23] Found parallel - /usr/local/bin/parallel
[12:57:23] Found freebayes - /usr/local/bin/freebayes
[12:57:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:23] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:23] Found gzip - /bin/gzip
[12:57:23] Found vt - /usr/local/bin/vt
[12:57:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:57:30] This is snippy 4.6.0Show full stderr[12:57:30] This is snippy 4.6.0
[12:57:30] Written by Torsten Seemann
[12:57:30] Obtained from https://github.com/tseemann/snippy
[12:57:30] Detected operating system: linux
[12:57:30] Enabling bundled linux tools.
[12:57:30] Found bwa - /usr/local/bin/bwa
[12:57:30] Found bcftools - /usr/local/bin/bcftools
[12:57:30] Found samtools - /usr/local/bin/samtools
[12:57:30] Found java - /usr/local/bin/java
[12:57:30] Found snpEff - /usr/local/bin/snpEff
[12:57:30] Found samclip - /usr/local/bin/samclip
[12:57:30] Found seqtk - /usr/local/bin/seqtk
[12:57:30] Found parallel - /usr/local/bin/parallel
[12:57:30] Found freebayes - /usr/local/bin/freebayes
[12:57:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:30] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:30] Found gzip - /bin/gzip
[12:57:30] Found vt - /usr/local/bin/vt
[12:57:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:33:00] This is snippy 4.6.0Show full stderr[13:33:00] This is snippy 4.6.0
[13:33:00] Written by Torsten Seemann
[13:33:00] Obtained from https://github.com/tseemann/snippy
[13:33:00] Detected operating system: linux
[13:33:00] Enabling bundled linux tools.
[13:33:00] Found bwa - /usr/local/bin/bwa
[13:33:00] Found bcftools - /usr/local/bin/bcftools
[13:33:00] Found samtools - /usr/local/bin/samtools
[13:33:00] Found java - /usr/local/bin/java
[13:33:00] Found snpEff - /usr/local/bin/snpEff
[13:33:00] Found samclip - /usr/local/bin/samclip
[13:33:00] Found seqtk - /usr/local/bin/seqtk
[13:33:00] Found parallel - /usr/local/bin/parallel
[13:33:00] Found freebayes - /usr/local/bin/freebayes
[13:33:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:33:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:33:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:33:00] Found vcfuniq - /usr/local/bin/vcfuniq
[13:33:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:33:00] Found gzip - /bin/gzip
[13:33:00] Found vt - /usr/local/bin/vt
[13:33:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:33:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:33:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:33:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:33:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:33:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:33:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:33:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:04:45] This is snippy 4.6.0Show full stderr[13:04:45] This is snippy 4.6.0
[13:04:45] Written by Torsten Seemann
[13:04:45] Obtained from https://github.com/tseemann/snippy
[13:04:45] Detected operating system: linux
[13:04:45] Enabling bundled linux tools.
[13:04:45] Found bwa - /usr/local/bin/bwa
[13:04:45] Found bcftools - /usr/local/bin/bcftools
[13:04:45] Found samtools - /usr/local/bin/samtools
[13:04:45] Found java - /usr/local/bin/java
[13:04:45] Found snpEff - /usr/local/bin/snpEff
[13:04:45] Found samclip - /usr/local/bin/samclip
[13:04:45] Found seqtk - /usr/local/bin/seqtk
[13:04:45] Found parallel - /usr/local/bin/parallel
[13:04:45] Found freebayes - /usr/local/bin/freebayes
[13:04:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:04:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:04:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:04:45] Found vcfuniq - /usr/local/bin/vcfuniq
[13:04:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:04:45] Found gzip - /bin/gzip
[13:04:45] Found vt - /usr/local/bin/vt
[13:04:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:04:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:04:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:04:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:04:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:04:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:04:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:04:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:51:33] This is snippy 4.6.0Show full stderr[12:51:33] This is snippy 4.6.0
[12:51:33] Written by Torsten Seemann
[12:51:33] Obtained from https://github.com/tseemann/snippy
[12:51:33] Detected operating system: linux
[12:51:33] Enabling bundled linux tools.
[12:51:33] Found bwa - /usr/local/bin/bwa
[12:51:33] Found bcftools - /usr/local/bin/bcftools
[12:51:33] Found samtools - /usr/local/bin/samtools
[12:51:33] Found java - /usr/local/bin/java
[12:51:33] Found snpEff - /usr/local/bin/snpEff
[12:51:33] Found samclip - /usr/local/bin/samclip
[12:51:33] Found seqtk - /usr/local/bin/seqtk
[12:51:33] Found parallel - /usr/local/bin/parallel
[12:51:33] Found freebayes - /usr/local/bin/freebayes
[12:51:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:51:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:51:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:51:33] Found vcfuniq - /usr/local/bin/vcfuniq
[12:51:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:51:33] Found gzip - /bin/gzip
[12:51:33] Found vt - /usr/local/bin/vt
[12:51:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:51:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:51:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:51:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:51:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:51:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:51:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:51:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:11:21] This is snippy 4.6.0Show full stderr[13:11:21] This is snippy 4.6.0
[13:11:21] Written by Torsten Seemann
[13:11:21] Obtained from https://github.com/tseemann/snippy
[13:11:21] Detected operating system: linux
[13:11:21] Enabling bundled linux tools.
[13:11:21] Found bwa - /usr/local/bin/bwa
[13:11:21] Found bcftools - /usr/local/bin/bcftools
[13:11:21] Found samtools - /usr/local/bin/samtools
[13:11:21] Found java - /usr/local/bin/java
[13:11:21] Found snpEff - /usr/local/bin/snpEff
[13:11:21] Found samclip - /usr/local/bin/samclip
[13:11:21] Found seqtk - /usr/local/bin/seqtk
[13:11:21] Found parallel - /usr/local/bin/parallel
[13:11:21] Found freebayes - /usr/local/bin/freebayes
[13:11:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:11:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:11:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:11:21] Found vcfuniq - /usr/local/bin/vcfuniq
[13:11:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:11:21] Found gzip - /bin/gzip
[13:11:21] Found vt - /usr/local/bin/vt
[13:11:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:11:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:11:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:11:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:11:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:11:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:11:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:11:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:17:15] This is snippy 4.6.0Show full stderr[13:17:15] This is snippy 4.6.0
[13:17:15] Written by Torsten Seemann
[13:17:15] Obtained from https://github.com/tseemann/snippy
[13:17:15] Detected operating system: linux
[13:17:15] Enabling bundled linux tools.
[13:17:15] Found bwa - /usr/local/bin/bwa
[13:17:15] Found bcftools - /usr/local/bin/bcftools
[13:17:15] Found samtools - /usr/local/bin/samtools
[13:17:15] Found java - /usr/local/bin/java
[13:17:15] Found snpEff - /usr/local/bin/snpEff
[13:17:15] Found samclip - /usr/local/bin/samclip
[13:17:15] Found seqtk - /usr/local/bin/seqtk
[13:17:15] Found parallel - /usr/local/bin/parallel
[13:17:15] Found freebayes - /usr/local/bin/freebayes
[13:17:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:17:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:17:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:17:15] Found vcfuniq - /usr/local/bin/vcfuniq
[13:17:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:17:15] Found gzip - /bin/gzip
[13:17:15] Found vt - /usr/local/bin/vt
[13:17:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:17:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:17:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:17:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:17:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:17:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:17:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:17:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:16:55] This is snippy 4.6.0Show full stderr[13:16:55] This is snippy 4.6.0
[13:16:55] Written by Torsten Seemann
[13:16:55] Obtained from https://github.com/tseemann/snippy
[13:16:55] Detected operating system: linux
[13:16:55] Enabling bundled linux tools.
[13:16:55] Found bwa - /usr/local/bin/bwa
[13:16:55] Found bcftools - /usr/local/bin/bcftools
[13:16:55] Found samtools - /usr/local/bin/samtools
[13:16:55] Found java - /usr/local/bin/java
[13:16:55] Found snpEff - /usr/local/bin/snpEff
[13:16:55] Found samclip - /usr/local/bin/samclip
[13:16:55] Found seqtk - /usr/local/bin/seqtk
[13:16:55] Found parallel - /usr/local/bin/parallel
[13:16:55] Found freebayes - /usr/local/bin/freebayes
[13:16:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:16:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:16:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:16:55] Found vcfuniq - /usr/local/bin/vcfuniq
[13:16:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:16:55] Found gzip - /bin/gzip
[13:16:55] Found vt - /usr/local/bin/vt
[13:16:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:16:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:16:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:16:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:16:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:17:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:17:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:17:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:16:50] This is snippy 4.6.0Show full stderr[13:16:50] This is snippy 4.6.0
[13:16:50] Written by Torsten Seemann
[13:16:50] Obtained from https://github.com/tseemann/snippy
[13:16:50] Detected operating system: linux
[13:16:50] Enabling bundled linux tools.
[13:16:50] Found bwa - /usr/local/bin/bwa
[13:16:50] Found bcftools - /usr/local/bin/bcftools
[13:16:50] Found samtools - /usr/local/bin/samtools
[13:16:50] Found java - /usr/local/bin/java
[13:16:50] Found snpEff - /usr/local/bin/snpEff
[13:16:50] Found samclip - /usr/local/bin/samclip
[13:16:50] Found seqtk - /usr/local/bin/seqtk
[13:16:50] Found parallel - /usr/local/bin/parallel
[13:16:50] Found freebayes - /usr/local/bin/freebayes
[13:16:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:16:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:16:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:16:50] Found vcfuniq - /usr/local/bin/vcfuniq
[13:16:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:16:50] Found gzip - /bin/gzip
[13:16:50] Found vt - /usr/local/bin/vt
[13:16:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:16:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:16:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:16:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:16:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:16:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:16:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:16:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:17:56] This is snippy 4.6.0Show full stderr[13:17:56] This is snippy 4.6.0
[13:17:56] Written by Torsten Seemann
[13:17:56] Obtained from https://github.com/tseemann/snippy
[13:17:56] Detected operating system: linux
[13:17:56] Enabling bundled linux tools.
[13:17:56] Found bwa - /usr/local/bin/bwa
[13:17:56] Found bcftools - /usr/local/bin/bcftools
[13:17:56] Found samtools - /usr/local/bin/samtools
[13:17:56] Found java - /usr/local/bin/java
[13:17:56] Found snpEff - /usr/local/bin/snpEff
[13:17:56] Found samclip - /usr/local/bin/samclip
[13:17:56] Found seqtk - /usr/local/bin/seqtk
[13:17:56] Found parallel - /usr/local/bin/parallel
[13:17:56] Found freebayes - /usr/local/bin/freebayes
[13:17:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:17:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:17:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:17:56] Found vcfuniq - /usr/local/bin/vcfuniq
[13:17:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:17:56] Found gzip - /bin/gzip
[13:17:56] Found vt - /usr/local/bin/vt
[13:17:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:17:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:17:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:17:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:17:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:17:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:17:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:17:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:25:02] This is snippy 4.6.0Show full stderr[13:25:02] This is snippy 4.6.0
[13:25:02] Written by Torsten Seemann
[13:25:02] Obtained from https://github.com/tseemann/snippy
[13:25:02] Detected operating system: linux
[13:25:02] Enabling bundled linux tools.
[13:25:02] Found bwa - /usr/local/bin/bwa
[13:25:02] Found bcftools - /usr/local/bin/bcftools
[13:25:02] Found samtools - /usr/local/bin/samtools
[13:25:02] Found java - /usr/local/bin/java
[13:25:02] Found snpEff - /usr/local/bin/snpEff
[13:25:02] Found samclip - /usr/local/bin/samclip
[13:25:02] Found seqtk - /usr/local/bin/seqtk
[13:25:02] Found parallel - /usr/local/bin/parallel
[13:25:02] Found freebayes - /usr/local/bin/freebayes
[13:25:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:25:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:25:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:25:02] Found vcfuniq - /usr/local/bin/vcfuniq
[13:25:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:25:02] Found gzip - /bin/gzip
[13:25:02] Found vt - /usr/local/bin/vt
[13:25:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:25:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:25:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:25:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:25:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:25:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:25:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:25:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:18:06] This is snippy 4.6.0Show full stderr[13:18:06] This is snippy 4.6.0
[13:18:06] Written by Torsten Seemann
[13:18:06] Obtained from https://github.com/tseemann/snippy
[13:18:06] Detected operating system: linux
[13:18:06] Enabling bundled linux tools.
[13:18:06] Found bwa - /usr/local/bin/bwa
[13:18:06] Found bcftools - /usr/local/bin/bcftools
[13:18:06] Found samtools - /usr/local/bin/samtools
[13:18:06] Found java - /usr/local/bin/java
[13:18:06] Found snpEff - /usr/local/bin/snpEff
[13:18:06] Found samclip - /usr/local/bin/samclip
[13:18:06] Found seqtk - /usr/local/bin/seqtk
[13:18:06] Found parallel - /usr/local/bin/parallel
[13:18:06] Found freebayes - /usr/local/bin/freebayes
[13:18:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:18:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:18:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:18:06] Found vcfuniq - /usr/local/bin/vcfuniq
[13:18:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:18:06] Found gzip - /bin/gzip
[13:18:06] Found vt - /usr/local/bin/vt
[13:18:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:18:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:18:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:18:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:18:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:18:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:18:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:18:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:23:54] This is snippy 4.6.0Show full stderr[13:23:54] This is snippy 4.6.0
[13:23:54] Written by Torsten Seemann
[13:23:54] Obtained from https://github.com/tseemann/snippy
[13:23:54] Detected operating system: linux
[13:23:54] Enabling bundled linux tools.
[13:23:54] Found bwa - /usr/local/bin/bwa
[13:23:54] Found bcftools - /usr/local/bin/bcftools
[13:23:54] Found samtools - /usr/local/bin/samtools
[13:23:54] Found java - /usr/local/bin/java
[13:23:54] Found snpEff - /usr/local/bin/snpEff
[13:23:54] Found samclip - /usr/local/bin/samclip
[13:23:54] Found seqtk - /usr/local/bin/seqtk
[13:23:54] Found parallel - /usr/local/bin/parallel
[13:23:54] Found freebayes - /usr/local/bin/freebayes
[13:23:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:23:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:23:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:23:54] Found vcfuniq - /usr/local/bin/vcfuniq
[13:23:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:23:54] Found gzip - /bin/gzip
[13:23:54] Found vt - /usr/local/bin/vt
[13:23:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:23:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:23:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:23:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:23:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:24:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:24:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:24:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:04:08] This is snippy 4.6.0Show full stderr[13:04:08] This is snippy 4.6.0
[13:04:08] Written by Torsten Seemann
[13:04:08] Obtained from https://github.com/tseemann/snippy
[13:04:08] Detected operating system: linux
[13:04:08] Enabling bundled linux tools.
[13:04:08] Found bwa - /usr/local/bin/bwa
[13:04:08] Found bcftools - /usr/local/bin/bcftools
[13:04:08] Found samtools - /usr/local/bin/samtools
[13:04:08] Found java - /usr/local/bin/java
[13:04:08] Found snpEff - /usr/local/bin/snpEff
[13:04:08] Found samclip - /usr/local/bin/samclip
[13:04:08] Found seqtk - /usr/local/bin/seqtk
[13:04:08] Found parallel - /usr/local/bin/parallel
[13:04:08] Found freebayes - /usr/local/bin/freebayes
[13:04:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:04:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:04:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:04:08] Found vcfuniq - /usr/local/bin/vcfuniq
[13:04:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:04:08] Found gzip - /bin/gzip
[13:04:08] Found vt - /usr/local/bin/vt
[13:04:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:04:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:04:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:04:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:04:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:04:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:04:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:04:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:09:56] This is snippy 4.6.0Show full stderr[13:09:56] This is snippy 4.6.0
[13:09:56] Written by Torsten Seemann
[13:09:56] Obtained from https://github.com/tseemann/snippy
[13:09:56] Detected operating system: linux
[13:09:56] Enabling bundled linux tools.
[13:09:56] Found bwa - /usr/local/bin/bwa
[13:09:56] Found bcftools - /usr/local/bin/bcftools
[13:09:56] Found samtools - /usr/local/bin/samtools
[13:09:56] Found java - /usr/local/bin/java
[13:09:56] Found snpEff - /usr/local/bin/snpEff
[13:09:56] Found samclip - /usr/local/bin/samclip
[13:09:56] Found seqtk - /usr/local/bin/seqtk
[13:09:56] Found parallel - /usr/local/bin/parallel
[13:09:56] Found freebayes - /usr/local/bin/freebayes
[13:09:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:09:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:09:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:09:56] Found vcfuniq - /usr/local/bin/vcfuniq
[13:09:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:09:56] Found gzip - /bin/gzip
[13:09:56] Found vt - /usr/local/bin/vt
[13:09:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:09:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:09:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:09:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:09:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:10:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:10:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:10:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:10:43] This is snippy 4.6.0Show full stderr[13:10:43] This is snippy 4.6.0
[13:10:43] Written by Torsten Seemann
[13:10:43] Obtained from https://github.com/tseemann/snippy
[13:10:43] Detected operating system: linux
[13:10:43] Enabling bundled linux tools.
[13:10:43] Found bwa - /usr/local/bin/bwa
[13:10:43] Found bcftools - /usr/local/bin/bcftools
[13:10:43] Found samtools - /usr/local/bin/samtools
[13:10:43] Found java - /usr/local/bin/java
[13:10:43] Found snpEff - /usr/local/bin/snpEff
[13:10:43] Found samclip - /usr/local/bin/samclip
[13:10:43] Found seqtk - /usr/local/bin/seqtk
[13:10:43] Found parallel - /usr/local/bin/parallel
[13:10:43] Found freebayes - /usr/local/bin/freebayes
[13:10:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:10:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:10:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:10:43] Found vcfuniq - /usr/local/bin/vcfuniq
[13:10:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:10:43] Found gzip - /bin/gzip
[13:10:43] Found vt - /usr/local/bin/vt
[13:10:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:10:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:10:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:10:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:10:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:10:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:10:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:10:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:25:39] This is snippy 4.6.0Show full stderr[13:25:39] This is snippy 4.6.0
[13:25:39] Written by Torsten Seemann
[13:25:39] Obtained from https://github.com/tseemann/snippy
[13:25:39] Detected operating system: linux
[13:25:39] Enabling bundled linux tools.
[13:25:39] Found bwa - /usr/local/bin/bwa
[13:25:39] Found bcftools - /usr/local/bin/bcftools
[13:25:39] Found samtools - /usr/local/bin/samtools
[13:25:39] Found java - /usr/local/bin/java
[13:25:39] Found snpEff - /usr/local/bin/snpEff
[13:25:39] Found samclip - /usr/local/bin/samclip
[13:25:39] Found seqtk - /usr/local/bin/seqtk
[13:25:39] Found parallel - /usr/local/bin/parallel
[13:25:39] Found freebayes - /usr/local/bin/freebayes
[13:25:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:25:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:25:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:25:39] Found vcfuniq - /usr/local/bin/vcfuniq
[13:25:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:25:39] Found gzip - /bin/gzip
[13:25:39] Found vt - /usr/local/bin/vt
[13:25:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:25:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:25:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:25:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:25:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:25:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:25:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:25:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:57:49] This is snippy 4.6.0Show full stderr[12:57:49] This is snippy 4.6.0
[12:57:49] Written by Torsten Seemann
[12:57:49] Obtained from https://github.com/tseemann/snippy
[12:57:49] Detected operating system: linux
[12:57:49] Enabling bundled linux tools.
[12:57:49] Found bwa - /usr/local/bin/bwa
[12:57:49] Found bcftools - /usr/local/bin/bcftools
[12:57:49] Found samtools - /usr/local/bin/samtools
[12:57:49] Found java - /usr/local/bin/java
[12:57:49] Found snpEff - /usr/local/bin/snpEff
[12:57:49] Found samclip - /usr/local/bin/samclip
[12:57:49] Found seqtk - /usr/local/bin/seqtk
[12:57:49] Found parallel - /usr/local/bin/parallel
[12:57:49] Found freebayes - /usr/local/bin/freebayes
[12:57:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:57:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:57:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:57:49] Found vcfuniq - /usr/local/bin/vcfuniq
[12:57:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:57:49] Found gzip - /bin/gzip
[12:57:49] Found vt - /usr/local/bin/vt
[12:57:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:57:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:57:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:57:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:57:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:57:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:57:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:57:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:58:14] This is snippy 4.6.0Show full stderr[12:58:14] This is snippy 4.6.0
[12:58:14] Written by Torsten Seemann
[12:58:14] Obtained from https://github.com/tseemann/snippy
[12:58:14] Detected operating system: linux
[12:58:14] Enabling bundled linux tools.
[12:58:14] Found bwa - /usr/local/bin/bwa
[12:58:14] Found bcftools - /usr/local/bin/bcftools
[12:58:14] Found samtools - /usr/local/bin/samtools
[12:58:14] Found java - /usr/local/bin/java
[12:58:14] Found snpEff - /usr/local/bin/snpEff
[12:58:14] Found samclip - /usr/local/bin/samclip
[12:58:14] Found seqtk - /usr/local/bin/seqtk
[12:58:14] Found parallel - /usr/local/bin/parallel
[12:58:14] Found freebayes - /usr/local/bin/freebayes
[12:58:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:58:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:58:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:58:14] Found vcfuniq - /usr/local/bin/vcfuniq
[12:58:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:58:14] Found gzip - /bin/gzip
[12:58:14] Found vt - /usr/local/bin/vt
[12:58:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:58:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:58:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:58:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:58:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:58:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:58:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:58:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:53:29] This is snippy 4.6.0Show full stderr[12:53:29] This is snippy 4.6.0
[12:53:29] Written by Torsten Seemann
[12:53:29] Obtained from https://github.com/tseemann/snippy
[12:53:29] Detected operating system: linux
[12:53:29] Enabling bundled linux tools.
[12:53:29] Found bwa - /usr/local/bin/bwa
[12:53:29] Found bcftools - /usr/local/bin/bcftools
[12:53:29] Found samtools - /usr/local/bin/samtools
[12:53:29] Found java - /usr/local/bin/java
[12:53:29] Found snpEff - /usr/local/bin/snpEff
[12:53:29] Found samclip - /usr/local/bin/samclip
[12:53:29] Found seqtk - /usr/local/bin/seqtk
[12:53:29] Found parallel - /usr/local/bin/parallel
[12:53:29] Found freebayes - /usr/local/bin/freebayes
[12:53:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:53:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:53:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:53:29] Found vcfuniq - /usr/local/bin/vcfuniq
[12:53:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:53:29] Found gzip - /bin/gzip
[12:53:29] Found vt - /usr/local/bin/vt
[12:53:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:53:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:53:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:53:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:53:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:53:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:53:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:53:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:54:11] This is snippy 4.6.0Show full stderr[12:54:11] This is snippy 4.6.0
[12:54:11] Written by Torsten Seemann
[12:54:11] Obtained from https://github.com/tseemann/snippy
[12:54:11] Detected operating system: linux
[12:54:11] Enabling bundled linux tools.
[12:54:11] Found bwa - /usr/local/bin/bwa
[12:54:11] Found bcftools - /usr/local/bin/bcftools
[12:54:11] Found samtools - /usr/local/bin/samtools
[12:54:11] Found java - /usr/local/bin/java
[12:54:11] Found snpEff - /usr/local/bin/snpEff
[12:54:11] Found samclip - /usr/local/bin/samclip
[12:54:11] Found seqtk - /usr/local/bin/seqtk
[12:54:11] Found parallel - /usr/local/bin/parallel
[12:54:11] Found freebayes - /usr/local/bin/freebayes
[12:54:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:54:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:54:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:54:11] Found vcfuniq - /usr/local/bin/vcfuniq
[12:54:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:54:11] Found gzip - /bin/gzip
[12:54:11] Found vt - /usr/local/bin/vt
[12:54:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:54:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:54:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:54:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:54:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:54:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:54:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:54:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:52:48] This is snippy 4.6.0Show full stderr[12:52:48] This is snippy 4.6.0
[12:52:48] Written by Torsten Seemann
[12:52:48] Obtained from https://github.com/tseemann/snippy
[12:52:48] Detected operating system: linux
[12:52:48] Enabling bundled linux tools.
[12:52:48] Found bwa - /usr/local/bin/bwa
[12:52:48] Found bcftools - /usr/local/bin/bcftools
[12:52:48] Found samtools - /usr/local/bin/samtools
[12:52:48] Found java - /usr/local/bin/java
[12:52:48] Found snpEff - /usr/local/bin/snpEff
[12:52:48] Found samclip - /usr/local/bin/samclip
[12:52:48] Found seqtk - /usr/local/bin/seqtk
[12:52:48] Found parallel - /usr/local/bin/parallel
[12:52:48] Found freebayes - /usr/local/bin/freebayes
[12:52:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:52:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:52:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:52:48] Found vcfuniq - /usr/local/bin/vcfuniq
[12:52:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:52:48] Found gzip - /bin/gzip
[12:52:48] Found vt - /usr/local/bin/vt
[12:52:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:52:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:52:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:52:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:52:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:52:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:52:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:52:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:58:50] This is snippy 4.6.0Show full stderr[12:58:50] This is snippy 4.6.0
[12:58:50] Written by Torsten Seemann
[12:58:50] Obtained from https://github.com/tseemann/snippy
[12:58:50] Detected operating system: linux
[12:58:50] Enabling bundled linux tools.
[12:58:50] Found bwa - /usr/local/bin/bwa
[12:58:50] Found bcftools - /usr/local/bin/bcftools
[12:58:50] Found samtools - /usr/local/bin/samtools
[12:58:50] Found java - /usr/local/bin/java
[12:58:50] Found snpEff - /usr/local/bin/snpEff
[12:58:50] Found samclip - /usr/local/bin/samclip
[12:58:50] Found seqtk - /usr/local/bin/seqtk
[12:58:50] Found parallel - /usr/local/bin/parallel
[12:58:50] Found freebayes - /usr/local/bin/freebayes
[12:58:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:58:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:58:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:58:50] Found vcfuniq - /usr/local/bin/vcfuniq
[12:58:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:58:50] Found gzip - /bin/gzip
[12:58:50] Found vt - /usr/local/bin/vt
[12:58:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:58:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:58:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:58:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:58:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:58:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:58:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:58:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:58:53] This is snippy 4.6.0Show full stderr[12:58:53] This is snippy 4.6.0
[12:58:53] Written by Torsten Seemann
[12:58:53] Obtained from https://github.com/tseemann/snippy
[12:58:53] Detected operating system: linux
[12:58:53] Enabling bundled linux tools.
[12:58:53] Found bwa - /usr/local/bin/bwa
[12:58:53] Found bcftools - /usr/local/bin/bcftools
[12:58:53] Found samtools - /usr/local/bin/samtools
[12:58:53] Found java - /usr/local/bin/java
[12:58:53] Found snpEff - /usr/local/bin/snpEff
[12:58:53] Found samclip - /usr/local/bin/samclip
[12:58:53] Found seqtk - /usr/local/bin/seqtk
[12:58:53] Found parallel - /usr/local/bin/parallel
[12:58:53] Found freebayes - /usr/local/bin/freebayes
[12:58:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:58:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:58:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:58:53] Found vcfuniq - /usr/local/bin/vcfuniq
[12:58:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:58:53] Found gzip - /bin/gzip
[12:58:53] Found vt - /usr/local/bin/vt
[12:58:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:58:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:58:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:58:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:58:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:58:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:58:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:58:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:58:59] This is snippy 4.6.0Show full stderr[12:58:59] This is snippy 4.6.0
[12:58:59] Written by Torsten Seemann
[12:58:59] Obtained from https://github.com/tseemann/snippy
[12:58:59] Detected operating system: linux
[12:58:59] Enabling bundled linux tools.
[12:58:59] Found bwa - /usr/local/bin/bwa
[12:58:59] Found bcftools - /usr/local/bin/bcftools
[12:58:59] Found samtools - /usr/local/bin/samtools
[12:58:59] Found java - /usr/local/bin/java
[12:58:59] Found snpEff - /usr/local/bin/snpEff
[12:58:59] Found samclip - /usr/local/bin/samclip
[12:58:59] Found seqtk - /usr/local/bin/seqtk
[12:58:59] Found parallel - /usr/local/bin/parallel
[12:58:59] Found freebayes - /usr/local/bin/freebayes
[12:58:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:58:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:58:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:58:59] Found vcfuniq - /usr/local/bin/vcfuniq
[12:58:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:58:59] Found gzip - /bin/gzip
[12:58:59] Found vt - /usr/local/bin/vt
[12:58:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:58:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:58:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:58:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:58:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:59:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:59:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:59:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:59:07] This is snippy 4.6.0Show full stderr[12:59:07] This is snippy 4.6.0
[12:59:07] Written by Torsten Seemann
[12:59:07] Obtained from https://github.com/tseemann/snippy
[12:59:07] Detected operating system: linux
[12:59:07] Enabling bundled linux tools.
[12:59:07] Found bwa - /usr/local/bin/bwa
[12:59:07] Found bcftools - /usr/local/bin/bcftools
[12:59:07] Found samtools - /usr/local/bin/samtools
[12:59:07] Found java - /usr/local/bin/java
[12:59:07] Found snpEff - /usr/local/bin/snpEff
[12:59:07] Found samclip - /usr/local/bin/samclip
[12:59:07] Found seqtk - /usr/local/bin/seqtk
[12:59:07] Found parallel - /usr/local/bin/parallel
[12:59:07] Found freebayes - /usr/local/bin/freebayes
[12:59:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:59:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:59:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:59:07] Found vcfuniq - /usr/local/bin/vcfuniq
[12:59:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:59:07] Found gzip - /bin/gzip
[12:59:07] Found vt - /usr/local/bin/vt
[12:59:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:59:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:59:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:59:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:59:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:59:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:59:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:59:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:53:44] This is snippy 4.6.0Show full stderr[12:53:44] This is snippy 4.6.0
[12:53:44] Written by Torsten Seemann
[12:53:44] Obtained from https://github.com/tseemann/snippy
[12:53:44] Detected operating system: linux
[12:53:44] Enabling bundled linux tools.
[12:53:44] Found bwa - /usr/local/bin/bwa
[12:53:44] Found bcftools - /usr/local/bin/bcftools
[12:53:44] Found samtools - /usr/local/bin/samtools
[12:53:44] Found java - /usr/local/bin/java
[12:53:44] Found snpEff - /usr/local/bin/snpEff
[12:53:44] Found samclip - /usr/local/bin/samclip
[12:53:44] Found seqtk - /usr/local/bin/seqtk
[12:53:44] Found parallel - /usr/local/bin/parallel
[12:53:44] Found freebayes - /usr/local/bin/freebayes
[12:53:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:53:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:53:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:53:44] Found vcfuniq - /usr/local/bin/vcfuniq
[12:53:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:53:44] Found gzip - /bin/gzip
[12:53:44] Found vt - /usr/local/bin/vt
[12:53:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:53:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:53:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:53:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:53:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:53:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:53:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:53:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:53:54] This is snippy 4.6.0Show full stderr[12:53:54] This is snippy 4.6.0
[12:53:54] Written by Torsten Seemann
[12:53:54] Obtained from https://github.com/tseemann/snippy
[12:53:54] Detected operating system: linux
[12:53:54] Enabling bundled linux tools.
[12:53:54] Found bwa - /usr/local/bin/bwa
[12:53:54] Found bcftools - /usr/local/bin/bcftools
[12:53:54] Found samtools - /usr/local/bin/samtools
[12:53:54] Found java - /usr/local/bin/java
[12:53:54] Found snpEff - /usr/local/bin/snpEff
[12:53:54] Found samclip - /usr/local/bin/samclip
[12:53:54] Found seqtk - /usr/local/bin/seqtk
[12:53:54] Found parallel - /usr/local/bin/parallel
[12:53:54] Found freebayes - /usr/local/bin/freebayes
[12:53:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:53:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:53:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:53:54] Found vcfuniq - /usr/local/bin/vcfuniq
[12:53:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:53:54] Found gzip - /bin/gzip
[12:53:54] Found vt - /usr/local/bin/vt
[12:53:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:53:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:53:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:53:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:53:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:53:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:53:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:53:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:53:57] This is snippy 4.6.0Show full stderr[12:53:57] This is snippy 4.6.0
[12:53:57] Written by Torsten Seemann
[12:53:57] Obtained from https://github.com/tseemann/snippy
[12:53:57] Detected operating system: linux
[12:53:57] Enabling bundled linux tools.
[12:53:57] Found bwa - /usr/local/bin/bwa
[12:53:57] Found bcftools - /usr/local/bin/bcftools
[12:53:57] Found samtools - /usr/local/bin/samtools
[12:53:57] Found java - /usr/local/bin/java
[12:53:57] Found snpEff - /usr/local/bin/snpEff
[12:53:57] Found samclip - /usr/local/bin/samclip
[12:53:57] Found seqtk - /usr/local/bin/seqtk
[12:53:57] Found parallel - /usr/local/bin/parallel
[12:53:57] Found freebayes - /usr/local/bin/freebayes
[12:53:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:53:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:53:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:53:57] Found vcfuniq - /usr/local/bin/vcfuniq
[12:53:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:53:58] Found gzip - /bin/gzip
[12:53:58] Found vt - /usr/local/bin/vt
[12:53:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:53:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:53:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:53:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:53:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:53:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:53:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:53:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:59:32] This is snippy 4.6.0Show full stderr[12:59:32] This is snippy 4.6.0
[12:59:32] Written by Torsten Seemann
[12:59:32] Obtained from https://github.com/tseemann/snippy
[12:59:32] Detected operating system: linux
[12:59:32] Enabling bundled linux tools.
[12:59:32] Found bwa - /usr/local/bin/bwa
[12:59:32] Found bcftools - /usr/local/bin/bcftools
[12:59:32] Found samtools - /usr/local/bin/samtools
[12:59:32] Found java - /usr/local/bin/java
[12:59:32] Found snpEff - /usr/local/bin/snpEff
[12:59:32] Found samclip - /usr/local/bin/samclip
[12:59:32] Found seqtk - /usr/local/bin/seqtk
[12:59:32] Found parallel - /usr/local/bin/parallel
[12:59:32] Found freebayes - /usr/local/bin/freebayes
[12:59:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:59:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:59:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:59:32] Found vcfuniq - /usr/local/bin/vcfuniq
[12:59:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:59:32] Found gzip - /bin/gzip
[12:59:32] Found vt - /usr/local/bin/vt
[12:59:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:59:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:59:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:59:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:59:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:59:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:59:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:59:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:59:46] This is snippy 4.6.0Show full stderr[12:59:46] This is snippy 4.6.0
[12:59:46] Written by Torsten Seemann
[12:59:46] Obtained from https://github.com/tseemann/snippy
[12:59:46] Detected operating system: linux
[12:59:46] Enabling bundled linux tools.
[12:59:46] Found bwa - /usr/local/bin/bwa
[12:59:46] Found bcftools - /usr/local/bin/bcftools
[12:59:46] Found samtools - /usr/local/bin/samtools
[12:59:46] Found java - /usr/local/bin/java
[12:59:46] Found snpEff - /usr/local/bin/snpEff
[12:59:46] Found samclip - /usr/local/bin/samclip
[12:59:46] Found seqtk - /usr/local/bin/seqtk
[12:59:46] Found parallel - /usr/local/bin/parallel
[12:59:46] Found freebayes - /usr/local/bin/freebayes
[12:59:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:59:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:59:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:59:46] Found vcfuniq - /usr/local/bin/vcfuniq
[12:59:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:59:46] Found gzip - /bin/gzip
[12:59:46] Found vt - /usr/local/bin/vt
[12:59:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:59:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:59:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:59:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:59:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:59:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:59:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:59:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:55:05] This is snippy 4.6.0Show full stderr[12:55:05] This is snippy 4.6.0
[12:55:05] Written by Torsten Seemann
[12:55:05] Obtained from https://github.com/tseemann/snippy
[12:55:05] Detected operating system: linux
[12:55:05] Enabling bundled linux tools.
[12:55:05] Found bwa - /usr/local/bin/bwa
[12:55:06] Found bcftools - /usr/local/bin/bcftools
[12:55:06] Found samtools - /usr/local/bin/samtools
[12:55:06] Found java - /usr/local/bin/java
[12:55:06] Found snpEff - /usr/local/bin/snpEff
[12:55:06] Found samclip - /usr/local/bin/samclip
[12:55:06] Found seqtk - /usr/local/bin/seqtk
[12:55:06] Found parallel - /usr/local/bin/parallel
[12:55:06] Found freebayes - /usr/local/bin/freebayes
[12:55:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:55:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:55:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:55:06] Found vcfuniq - /usr/local/bin/vcfuniq
[12:55:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:55:06] Found gzip - /bin/gzip
[12:55:06] Found vt - /usr/local/bin/vt
[12:55:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:55:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:55:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:55:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:55:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:55:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:55:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:55:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:55:22] This is snippy 4.6.0Show full stderr[12:55:22] This is snippy 4.6.0
[12:55:22] Written by Torsten Seemann
[12:55:22] Obtained from https://github.com/tseemann/snippy
[12:55:22] Detected operating system: linux
[12:55:22] Enabling bundled linux tools.
[12:55:22] Found bwa - /usr/local/bin/bwa
[12:55:22] Found bcftools - /usr/local/bin/bcftools
[12:55:23] Found samtools - /usr/local/bin/samtools
[12:55:23] Found java - /usr/local/bin/java
[12:55:23] Found snpEff - /usr/local/bin/snpEff
[12:55:23] Found samclip - /usr/local/bin/samclip
[12:55:23] Found seqtk - /usr/local/bin/seqtk
[12:55:23] Found parallel - /usr/local/bin/parallel
[12:55:23] Found freebayes - /usr/local/bin/freebayes
[12:55:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:55:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:55:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:55:23] Found vcfuniq - /usr/local/bin/vcfuniq
[12:55:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:55:23] Found gzip - /bin/gzip
[12:55:23] Found vt - /usr/local/bin/vt
[12:55:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:55:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:55:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:55:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:55:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:55:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:55:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:55:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:55:33] This is snippy 4.6.0Show full stderr[12:55:33] This is snippy 4.6.0
[12:55:33] Written by Torsten Seemann
[12:55:33] Obtained from https://github.com/tseemann/snippy
[12:55:33] Detected operating system: linux
[12:55:33] Enabling bundled linux tools.
[12:55:33] Found bwa - /usr/local/bin/bwa
[12:55:33] Found bcftools - /usr/local/bin/bcftools
[12:55:33] Found samtools - /usr/local/bin/samtools
[12:55:33] Found java - /usr/local/bin/java
[12:55:33] Found snpEff - /usr/local/bin/snpEff
[12:55:33] Found samclip - /usr/local/bin/samclip
[12:55:33] Found seqtk - /usr/local/bin/seqtk
[12:55:33] Found parallel - /usr/local/bin/parallel
[12:55:33] Found freebayes - /usr/local/bin/freebayes
[12:55:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:55:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:55:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:55:33] Found vcfuniq - /usr/local/bin/vcfuniq
[12:55:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:55:33] Found gzip - /bin/gzip
[12:55:33] Found vt - /usr/local/bin/vt
[12:55:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:55:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:55:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:55:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:55:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:55:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:55:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:55:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:55:32] This is snippy 4.6.0Show full stderr[12:55:32] This is snippy 4.6.0
[12:55:32] Written by Torsten Seemann
[12:55:32] Obtained from https://github.com/tseemann/snippy
[12:55:32] Detected operating system: linux
[12:55:32] Enabling bundled linux tools.
[12:55:32] Found bwa - /usr/local/bin/bwa
[12:55:32] Found bcftools - /usr/local/bin/bcftools
[12:55:32] Found samtools - /usr/local/bin/samtools
[12:55:32] Found java - /usr/local/bin/java
[12:55:32] Found snpEff - /usr/local/bin/snpEff
[12:55:32] Found samclip - /usr/local/bin/samclip
[12:55:32] Found seqtk - /usr/local/bin/seqtk
[12:55:32] Found parallel - /usr/local/bin/parallel
[12:55:32] Found freebayes - /usr/local/bin/freebayes
[12:55:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:55:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:55:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:55:33] Found vcfuniq - /usr/local/bin/vcfuniq
[12:55:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:55:33] Found gzip - /bin/gzip
[12:55:33] Found vt - /usr/local/bin/vt
[12:55:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:55:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:55:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:55:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:55:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:55:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:55:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:55:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [13:00:17] This is snippy 4.6.0Show full stderr[13:00:17] This is snippy 4.6.0
[13:00:17] Written by Torsten Seemann
[13:00:17] Obtained from https://github.com/tseemann/snippy
[13:00:17] Detected operating system: linux
[13:00:17] Enabling bundled linux tools.
[13:00:17] Found bwa - /usr/local/bin/bwa
[13:00:17] Found bcftools - /usr/local/bin/bcftools
[13:00:17] Found samtools - /usr/local/bin/samtools
[13:00:17] Found java - /usr/local/bin/java
[13:00:17] Found snpEff - /usr/local/bin/snpEff
[13:00:17] Found samclip - /usr/local/bin/samclip
[13:00:17] Found seqtk - /usr/local/bin/seqtk
[13:00:17] Found parallel - /usr/local/bin/parallel
[13:00:17] Found freebayes - /usr/local/bin/freebayes
[13:00:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:00:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:00:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:00:17] Found vcfuniq - /usr/local/bin/vcfuniq
[13:00:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:00:17] Found gzip - /bin/gzip
[13:00:17] Found vt - /usr/local/bin/vt
[13:00:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:00:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:00:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:00:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:00:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:00:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:00:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:00:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:40:20] This is snippy 4.6.0Show full stderr[19:40:20] This is snippy 4.6.0
[19:40:20] Written by Torsten Seemann
[19:40:20] Obtained from https://github.com/tseemann/snippy
[19:40:20] Detected operating system: linux
[19:40:20] Enabling bundled linux tools.
[19:40:20] Found bwa - /usr/local/bin/bwa
[19:40:20] Found bcftools - /usr/local/bin/bcftools
[19:40:20] Found samtools - /usr/local/bin/samtools
[19:40:20] Found java - /usr/local/bin/java
[19:40:20] Found snpEff - /usr/local/bin/snpEff
[19:40:20] Found samclip - /usr/local/bin/samclip
[19:40:20] Found seqtk - /usr/local/bin/seqtk
[19:40:20] Found parallel - /usr/local/bin/parallel
[19:40:20] Found freebayes - /usr/local/bin/freebayes
[19:40:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:20] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:20] Found gzip - /bin/gzip
[19:40:20] Found vt - /usr/local/bin/vt
[19:40:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:40:52] This is snippy 4.6.0Show full stderr[19:40:52] This is snippy 4.6.0
[19:40:52] Written by Torsten Seemann
[19:40:52] Obtained from https://github.com/tseemann/snippy
[19:40:52] Detected operating system: linux
[19:40:52] Enabling bundled linux tools.
[19:40:52] Found bwa - /usr/local/bin/bwa
[19:40:52] Found bcftools - /usr/local/bin/bcftools
[19:40:52] Found samtools - /usr/local/bin/samtools
[19:40:52] Found java - /usr/local/bin/java
[19:40:52] Found snpEff - /usr/local/bin/snpEff
[19:40:52] Found samclip - /usr/local/bin/samclip
[19:40:52] Found seqtk - /usr/local/bin/seqtk
[19:40:52] Found parallel - /usr/local/bin/parallel
[19:40:52] Found freebayes - /usr/local/bin/freebayes
[19:40:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:52] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:52] Found gzip - /bin/gzip
[19:40:52] Found vt - /usr/local/bin/vt
[19:40:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:46:59] This is snippy 4.6.0Show full stderr[19:46:59] This is snippy 4.6.0
[19:46:59] Written by Torsten Seemann
[19:46:59] Obtained from https://github.com/tseemann/snippy
[19:46:59] Detected operating system: linux
[19:46:59] Enabling bundled linux tools.
[19:46:59] Found bwa - /usr/local/bin/bwa
[19:46:59] Found bcftools - /usr/local/bin/bcftools
[19:46:59] Found samtools - /usr/local/bin/samtools
[19:46:59] Found java - /usr/local/bin/java
[19:46:59] Found snpEff - /usr/local/bin/snpEff
[19:46:59] Found samclip - /usr/local/bin/samclip
[19:46:59] Found seqtk - /usr/local/bin/seqtk
[19:46:59] Found parallel - /usr/local/bin/parallel
[19:46:59] Found freebayes - /usr/local/bin/freebayes
[19:46:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:46:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:46:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:46:59] Found vcfuniq - /usr/local/bin/vcfuniq
[19:46:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:46:59] Found gzip - /bin/gzip
[19:46:59] Found vt - /usr/local/bin/vt
[19:46:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:46:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:47:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:47:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:47:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:47:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:47:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:47:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:47:00] This is snippy 4.6.0Show full stderr[19:47:00] This is snippy 4.6.0
[19:47:00] Written by Torsten Seemann
[19:47:00] Obtained from https://github.com/tseemann/snippy
[19:47:00] Detected operating system: linux
[19:47:00] Enabling bundled linux tools.
[19:47:00] Found bwa - /usr/local/bin/bwa
[19:47:00] Found bcftools - /usr/local/bin/bcftools
[19:47:00] Found samtools - /usr/local/bin/samtools
[19:47:00] Found java - /usr/local/bin/java
[19:47:00] Found snpEff - /usr/local/bin/snpEff
[19:47:00] Found samclip - /usr/local/bin/samclip
[19:47:00] Found seqtk - /usr/local/bin/seqtk
[19:47:00] Found parallel - /usr/local/bin/parallel
[19:47:00] Found freebayes - /usr/local/bin/freebayes
[19:47:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:47:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:47:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:47:00] Found vcfuniq - /usr/local/bin/vcfuniq
[19:47:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:47:00] Found gzip - /bin/gzip
[19:47:00] Found vt - /usr/local/bin/vt
[19:47:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:47:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:47:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:47:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:47:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:47:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:47:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:47:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:40:58] This is snippy 4.6.0Show full stderr[19:40:58] This is snippy 4.6.0
[19:40:58] Written by Torsten Seemann
[19:40:58] Obtained from https://github.com/tseemann/snippy
[19:40:58] Detected operating system: linux
[19:40:58] Enabling bundled linux tools.
[19:40:58] Found bwa - /usr/local/bin/bwa
[19:40:58] Found bcftools - /usr/local/bin/bcftools
[19:40:58] Found samtools - /usr/local/bin/samtools
[19:40:58] Found java - /usr/local/bin/java
[19:40:58] Found snpEff - /usr/local/bin/snpEff
[19:40:58] Found samclip - /usr/local/bin/samclip
[19:40:58] Found seqtk - /usr/local/bin/seqtk
[19:40:58] Found parallel - /usr/local/bin/parallel
[19:40:58] Found freebayes - /usr/local/bin/freebayes
[19:40:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:58] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:58] Found gzip - /bin/gzip
[19:40:58] Found vt - /usr/local/bin/vt
[19:40:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:41:08] This is snippy 4.6.0Show full stderr[19:41:08] This is snippy 4.6.0
[19:41:08] Written by Torsten Seemann
[19:41:08] Obtained from https://github.com/tseemann/snippy
[19:41:08] Detected operating system: linux
[19:41:08] Enabling bundled linux tools.
[19:41:08] Found bwa - /usr/local/bin/bwa
[19:41:08] Found bcftools - /usr/local/bin/bcftools
[19:41:08] Found samtools - /usr/local/bin/samtools
[19:41:08] Found java - /usr/local/bin/java
[19:41:08] Found snpEff - /usr/local/bin/snpEff
[19:41:08] Found samclip - /usr/local/bin/samclip
[19:41:08] Found seqtk - /usr/local/bin/seqtk
[19:41:08] Found parallel - /usr/local/bin/parallel
[19:41:08] Found freebayes - /usr/local/bin/freebayes
[19:41:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:41:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:41:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:41:08] Found vcfuniq - /usr/local/bin/vcfuniq
[19:41:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:41:08] Found gzip - /bin/gzip
[19:41:08] Found vt - /usr/local/bin/vt
[19:41:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:41:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:41:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:41:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:41:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:41:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:41:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:41:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:52:24] This is snippy 4.6.0Show full stderr[19:52:24] This is snippy 4.6.0
[19:52:24] Written by Torsten Seemann
[19:52:24] Obtained from https://github.com/tseemann/snippy
[19:52:24] Detected operating system: linux
[19:52:24] Enabling bundled linux tools.
[19:52:24] Found bwa - /usr/local/bin/bwa
[19:52:24] Found bcftools - /usr/local/bin/bcftools
[19:52:24] Found samtools - /usr/local/bin/samtools
[19:52:24] Found java - /usr/local/bin/java
[19:52:24] Found snpEff - /usr/local/bin/snpEff
[19:52:24] Found samclip - /usr/local/bin/samclip
[19:52:24] Found seqtk - /usr/local/bin/seqtk
[19:52:24] Found parallel - /usr/local/bin/parallel
[19:52:24] Found freebayes - /usr/local/bin/freebayes
[19:52:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:52:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:52:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:52:24] Found vcfuniq - /usr/local/bin/vcfuniq
[19:52:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:52:24] Found gzip - /bin/gzip
[19:52:24] Found vt - /usr/local/bin/vt
[19:52:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:52:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:52:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:52:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:52:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:52:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:52:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:52:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:40:23] This is snippy 4.6.0Show full stderr[19:40:23] This is snippy 4.6.0
[19:40:23] Written by Torsten Seemann
[19:40:23] Obtained from https://github.com/tseemann/snippy
[19:40:23] Detected operating system: linux
[19:40:23] Enabling bundled linux tools.
[19:40:23] Found bwa - /usr/local/bin/bwa
[19:40:23] Found bcftools - /usr/local/bin/bcftools
[19:40:23] Found samtools - /usr/local/bin/samtools
[19:40:23] Found java - /usr/local/bin/java
[19:40:23] Found snpEff - /usr/local/bin/snpEff
[19:40:23] Found samclip - /usr/local/bin/samclip
[19:40:23] Found seqtk - /usr/local/bin/seqtk
[19:40:23] Found parallel - /usr/local/bin/parallel
[19:40:23] Found freebayes - /usr/local/bin/freebayes
[19:40:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:23] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:23] Found gzip - /bin/gzip
[19:40:23] Found vt - /usr/local/bin/vt
[19:40:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:46:27] This is snippy 4.6.0Show full stderr[19:46:27] This is snippy 4.6.0
[19:46:27] Written by Torsten Seemann
[19:46:27] Obtained from https://github.com/tseemann/snippy
[19:46:27] Detected operating system: linux
[19:46:27] Enabling bundled linux tools.
[19:46:27] Found bwa - /usr/local/bin/bwa
[19:46:27] Found bcftools - /usr/local/bin/bcftools
[19:46:27] Found samtools - /usr/local/bin/samtools
[19:46:27] Found java - /usr/local/bin/java
[19:46:27] Found snpEff - /usr/local/bin/snpEff
[19:46:27] Found samclip - /usr/local/bin/samclip
[19:46:27] Found seqtk - /usr/local/bin/seqtk
[19:46:27] Found parallel - /usr/local/bin/parallel
[19:46:27] Found freebayes - /usr/local/bin/freebayes
[19:46:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:46:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:46:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:46:27] Found vcfuniq - /usr/local/bin/vcfuniq
[19:46:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:46:27] Found gzip - /bin/gzip
[19:46:27] Found vt - /usr/local/bin/vt
[19:46:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:46:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:46:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:46:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:46:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:46:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:46:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:46:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:40:42] This is snippy 4.6.0Show full stderr[19:40:42] This is snippy 4.6.0
[19:40:42] Written by Torsten Seemann
[19:40:42] Obtained from https://github.com/tseemann/snippy
[19:40:42] Detected operating system: linux
[19:40:42] Enabling bundled linux tools.
[19:40:42] Found bwa - /usr/local/bin/bwa
[19:40:42] Found bcftools - /usr/local/bin/bcftools
[19:40:42] Found samtools - /usr/local/bin/samtools
[19:40:42] Found java - /usr/local/bin/java
[19:40:42] Found snpEff - /usr/local/bin/snpEff
[19:40:42] Found samclip - /usr/local/bin/samclip
[19:40:42] Found seqtk - /usr/local/bin/seqtk
[19:40:42] Found parallel - /usr/local/bin/parallel
[19:40:42] Found freebayes - /usr/local/bin/freebayes
[19:40:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:42] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:42] Found gzip - /bin/gzip
[19:40:42] Found vt - /usr/local/bin/vt
[19:40:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:46:24] This is snippy 4.6.0Show full stderr[19:46:24] This is snippy 4.6.0
[19:46:24] Written by Torsten Seemann
[19:46:24] Obtained from https://github.com/tseemann/snippy
[19:46:24] Detected operating system: linux
[19:46:24] Enabling bundled linux tools.
[19:46:24] Found bwa - /usr/local/bin/bwa
[19:46:24] Found bcftools - /usr/local/bin/bcftools
[19:46:24] Found samtools - /usr/local/bin/samtools
[19:46:24] Found java - /usr/local/bin/java
[19:46:24] Found snpEff - /usr/local/bin/snpEff
[19:46:24] Found samclip - /usr/local/bin/samclip
[19:46:24] Found seqtk - /usr/local/bin/seqtk
[19:46:24] Found parallel - /usr/local/bin/parallel
[19:46:24] Found freebayes - /usr/local/bin/freebayes
[19:46:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:46:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:46:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:46:24] Found vcfuniq - /usr/local/bin/vcfuniq
[19:46:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:46:24] Found gzip - /bin/gzip
[19:46:24] Found vt - /usr/local/bin/vt
[19:46:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:46:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:46:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:46:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:46:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:46:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:46:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:46:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:55:33] This is snippy 4.6.0Show full stderr[06:55:33] This is snippy 4.6.0
[06:55:33] Written by Torsten Seemann
[06:55:33] Obtained from https://github.com/tseemann/snippy
[06:55:33] Detected operating system: linux
[06:55:33] Enabling bundled linux tools.
[06:55:33] Found bwa - /usr/local/bin/bwa
[06:55:33] Found bcftools - /usr/local/bin/bcftools
[06:55:33] Found samtools - /usr/local/bin/samtools
[06:55:33] Found java - /usr/local/bin/java
[06:55:33] Found snpEff - /usr/local/bin/snpEff
[06:55:33] Found samclip - /usr/local/bin/samclip
[06:55:33] Found seqtk - /usr/local/bin/seqtk
[06:55:33] Found parallel - /usr/local/bin/parallel
[06:55:33] Found freebayes - /usr/local/bin/freebayes
[06:55:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:55:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:55:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:55:33] Found vcfuniq - /usr/local/bin/vcfuniq
[06:55:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:55:33] Found gzip - /bin/gzip
[06:55:33] Found vt - /usr/local/bin/vt
[06:55:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:55:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:55:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:55:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:55:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:55:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:55:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:55:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:06:51] This is snippy 4.6.0Show full stderr[07:06:51] This is snippy 4.6.0
[07:06:51] Written by Torsten Seemann
[07:06:51] Obtained from https://github.com/tseemann/snippy
[07:06:51] Detected operating system: linux
[07:06:51] Enabling bundled linux tools.
[07:06:51] Found bwa - /usr/local/bin/bwa
[07:06:51] Found bcftools - /usr/local/bin/bcftools
[07:06:51] Found samtools - /usr/local/bin/samtools
[07:06:51] Found java - /usr/local/bin/java
[07:06:51] Found snpEff - /usr/local/bin/snpEff
[07:06:51] Found samclip - /usr/local/bin/samclip
[07:06:51] Found seqtk - /usr/local/bin/seqtk
[07:06:51] Found parallel - /usr/local/bin/parallel
[07:06:51] Found freebayes - /usr/local/bin/freebayes
[07:06:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:06:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:06:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:06:51] Found vcfuniq - /usr/local/bin/vcfuniq
[07:06:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:06:51] Found gzip - /bin/gzip
[07:06:51] Found vt - /usr/local/bin/vt
[07:06:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:06:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:06:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:06:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:06:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:06:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:06:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:06:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:07:06] This is snippy 4.6.0Show full stderr[07:07:06] This is snippy 4.6.0
[07:07:06] Written by Torsten Seemann
[07:07:06] Obtained from https://github.com/tseemann/snippy
[07:07:06] Detected operating system: linux
[07:07:06] Enabling bundled linux tools.
[07:07:06] Found bwa - /usr/local/bin/bwa
[07:07:06] Found bcftools - /usr/local/bin/bcftools
[07:07:06] Found samtools - /usr/local/bin/samtools
[07:07:06] Found java - /usr/local/bin/java
[07:07:06] Found snpEff - /usr/local/bin/snpEff
[07:07:06] Found samclip - /usr/local/bin/samclip
[07:07:06] Found seqtk - /usr/local/bin/seqtk
[07:07:06] Found parallel - /usr/local/bin/parallel
[07:07:06] Found freebayes - /usr/local/bin/freebayes
[07:07:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:07:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:07:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:07:06] Found vcfuniq - /usr/local/bin/vcfuniq
[07:07:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:07:06] Found gzip - /bin/gzip
[07:07:06] Found vt - /usr/local/bin/vt
[07:07:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:07:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:07:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:07:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:07:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:07:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:07:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:07:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:24:06] This is snippy 4.6.0Show full stderr[07:24:06] This is snippy 4.6.0
[07:24:06] Written by Torsten Seemann
[07:24:06] Obtained from https://github.com/tseemann/snippy
[07:24:06] Detected operating system: linux
[07:24:06] Enabling bundled linux tools.
[07:24:06] Found bwa - /usr/local/bin/bwa
[07:24:06] Found bcftools - /usr/local/bin/bcftools
[07:24:06] Found samtools - /usr/local/bin/samtools
[07:24:06] Found java - /usr/local/bin/java
[07:24:06] Found snpEff - /usr/local/bin/snpEff
[07:24:06] Found samclip - /usr/local/bin/samclip
[07:24:06] Found seqtk - /usr/local/bin/seqtk
[07:24:06] Found parallel - /usr/local/bin/parallel
[07:24:06] Found freebayes - /usr/local/bin/freebayes
[07:24:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:24:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:24:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:24:06] Found vcfuniq - /usr/local/bin/vcfuniq
[07:24:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:24:06] Found gzip - /bin/gzip
[07:24:06] Found vt - /usr/local/bin/vt
[07:24:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:24:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:24:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:24:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:24:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:24:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:24:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:24:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:02:30] This is snippy 4.6.0Show full stderr[08:02:30] This is snippy 4.6.0
[08:02:30] Written by Torsten Seemann
[08:02:30] Obtained from https://github.com/tseemann/snippy
[08:02:30] Detected operating system: linux
[08:02:30] Enabling bundled linux tools.
[08:02:30] Found bwa - /usr/local/bin/bwa
[08:02:30] Found bcftools - /usr/local/bin/bcftools
[08:02:30] Found samtools - /usr/local/bin/samtools
[08:02:30] Found java - /usr/local/bin/java
[08:02:30] Found snpEff - /usr/local/bin/snpEff
[08:02:30] Found samclip - /usr/local/bin/samclip
[08:02:30] Found seqtk - /usr/local/bin/seqtk
[08:02:30] Found parallel - /usr/local/bin/parallel
[08:02:30] Found freebayes - /usr/local/bin/freebayes
[08:02:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:02:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:02:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:02:30] Found vcfuniq - /usr/local/bin/vcfuniq
[08:02:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:02:30] Found gzip - /bin/gzip
[08:02:30] Found vt - /usr/local/bin/vt
[08:02:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:02:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:02:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:02:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:02:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:02:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:02:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:02:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:08:52] This is snippy 4.6.0Show full stderr[08:08:52] This is snippy 4.6.0
[08:08:52] Written by Torsten Seemann
[08:08:52] Obtained from https://github.com/tseemann/snippy
[08:08:52] Detected operating system: linux
[08:08:52] Enabling bundled linux tools.
[08:08:52] Found bwa - /usr/local/bin/bwa
[08:08:52] Found bcftools - /usr/local/bin/bcftools
[08:08:52] Found samtools - /usr/local/bin/samtools
[08:08:52] Found java - /usr/local/bin/java
[08:08:52] Found snpEff - /usr/local/bin/snpEff
[08:08:52] Found samclip - /usr/local/bin/samclip
[08:08:52] Found seqtk - /usr/local/bin/seqtk
[08:08:52] Found parallel - /usr/local/bin/parallel
[08:08:52] Found freebayes - /usr/local/bin/freebayes
[08:08:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:08:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:08:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:08:52] Found vcfuniq - /usr/local/bin/vcfuniq
[08:08:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:08:52] Found gzip - /bin/gzip
[08:08:52] Found vt - /usr/local/bin/vt
[08:08:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:08:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:08:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:08:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:08:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:08:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:08:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:08:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:14:54] This is snippy 4.6.0Show full stderr[08:14:54] This is snippy 4.6.0
[08:14:54] Written by Torsten Seemann
[08:14:54] Obtained from https://github.com/tseemann/snippy
[08:14:54] Detected operating system: linux
[08:14:54] Enabling bundled linux tools.
[08:14:54] Found bwa - /usr/local/bin/bwa
[08:14:54] Found bcftools - /usr/local/bin/bcftools
[08:14:54] Found samtools - /usr/local/bin/samtools
[08:14:54] Found java - /usr/local/bin/java
[08:14:54] Found snpEff - /usr/local/bin/snpEff
[08:14:54] Found samclip - /usr/local/bin/samclip
[08:14:54] Found seqtk - /usr/local/bin/seqtk
[08:14:54] Found parallel - /usr/local/bin/parallel
[08:14:54] Found freebayes - /usr/local/bin/freebayes
[08:14:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:14:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:14:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:14:54] Found vcfuniq - /usr/local/bin/vcfuniq
[08:14:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:14:54] Found gzip - /bin/gzip
[08:14:54] Found vt - /usr/local/bin/vt
[08:14:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:14:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:14:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:14:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:14:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:14:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:14:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:14:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:15:52] This is snippy 4.6.0Show full stderr[08:15:52] This is snippy 4.6.0
[08:15:52] Written by Torsten Seemann
[08:15:52] Obtained from https://github.com/tseemann/snippy
[08:15:52] Detected operating system: linux
[08:15:52] Enabling bundled linux tools.
[08:15:52] Found bwa - /usr/local/bin/bwa
[08:15:52] Found bcftools - /usr/local/bin/bcftools
[08:15:52] Found samtools - /usr/local/bin/samtools
[08:15:52] Found java - /usr/local/bin/java
[08:15:52] Found snpEff - /usr/local/bin/snpEff
[08:15:52] Found samclip - /usr/local/bin/samclip
[08:15:52] Found seqtk - /usr/local/bin/seqtk
[08:15:52] Found parallel - /usr/local/bin/parallel
[08:15:52] Found freebayes - /usr/local/bin/freebayes
[08:15:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:15:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:15:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:15:52] Found vcfuniq - /usr/local/bin/vcfuniq
[08:15:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:15:52] Found gzip - /bin/gzip
[08:15:52] Found vt - /usr/local/bin/vt
[08:15:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:15:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:15:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:15:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:15:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:15:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:15:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:15:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:42:07] This is snippy 4.6.0Show full stderr[08:42:07] This is snippy 4.6.0
[08:42:07] Written by Torsten Seemann
[08:42:07] Obtained from https://github.com/tseemann/snippy
[08:42:07] Detected operating system: linux
[08:42:07] Enabling bundled linux tools.
[08:42:07] Found bwa - /usr/local/bin/bwa
[08:42:07] Found bcftools - /usr/local/bin/bcftools
[08:42:07] Found samtools - /usr/local/bin/samtools
[08:42:07] Found java - /usr/local/bin/java
[08:42:07] Found snpEff - /usr/local/bin/snpEff
[08:42:07] Found samclip - /usr/local/bin/samclip
[08:42:07] Found seqtk - /usr/local/bin/seqtk
[08:42:07] Found parallel - /usr/local/bin/parallel
[08:42:07] Found freebayes - /usr/local/bin/freebayes
[08:42:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:42:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:42:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:42:07] Found vcfuniq - /usr/local/bin/vcfuniq
[08:42:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:42:07] Found gzip - /bin/gzip
[08:42:07] Found vt - /usr/local/bin/vt
[08:42:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:42:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:42:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:42:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:42:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:42:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:42:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:42:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:48:49] This is snippy 4.6.0Show full stderr[08:48:49] This is snippy 4.6.0
[08:48:49] Written by Torsten Seemann
[08:48:49] Obtained from https://github.com/tseemann/snippy
[08:48:49] Detected operating system: linux
[08:48:49] Enabling bundled linux tools.
[08:48:49] Found bwa - /usr/local/bin/bwa
[08:48:49] Found bcftools - /usr/local/bin/bcftools
[08:48:49] Found samtools - /usr/local/bin/samtools
[08:48:49] Found java - /usr/local/bin/java
[08:48:49] Found snpEff - /usr/local/bin/snpEff
[08:48:49] Found samclip - /usr/local/bin/samclip
[08:48:49] Found seqtk - /usr/local/bin/seqtk
[08:48:49] Found parallel - /usr/local/bin/parallel
[08:48:49] Found freebayes - /usr/local/bin/freebayes
[08:48:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:48:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:48:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:48:49] Found vcfuniq - /usr/local/bin/vcfuniq
[08:48:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:48:49] Found gzip - /bin/gzip
[08:48:49] Found vt - /usr/local/bin/vt
[08:48:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:48:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:48:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:48:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:48:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:48:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:48:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:48:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [08:48:37] This is snippy 4.6.0Show full stderr[08:48:37] This is snippy 4.6.0
[08:48:37] Written by Torsten Seemann
[08:48:37] Obtained from https://github.com/tseemann/snippy
[08:48:37] Detected operating system: linux
[08:48:37] Enabling bundled linux tools.
[08:48:37] Found bwa - /usr/local/bin/bwa
[08:48:37] Found bcftools - /usr/local/bin/bcftools
[08:48:37] Found samtools - /usr/local/bin/samtools
[08:48:37] Found java - /usr/local/bin/java
[08:48:37] Found snpEff - /usr/local/bin/snpEff
[08:48:37] Found samclip - /usr/local/bin/samclip
[08:48:37] Found seqtk - /usr/local/bin/seqtk
[08:48:37] Found parallel - /usr/local/bin/parallel
[08:48:37] Found freebayes - /usr/local/bin/freebayes
[08:48:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:48:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:48:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:48:37] Found vcfuniq - /usr/local/bin/vcfuniq
[08:48:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:48:37] Found gzip - /bin/gzip
[08:48:37] Found vt - /usr/local/bin/vt
[08:48:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:48:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:48:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:48:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:48:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:48:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:48:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:48:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [09:01:59] This is snippy 4.6.0Show full stderr[09:01:59] This is snippy 4.6.0
[09:01:59] Written by Torsten Seemann
[09:01:59] Obtained from https://github.com/tseemann/snippy
[09:01:59] Detected operating system: linux
[09:01:59] Enabling bundled linux tools.
[09:01:59] Found bwa - /usr/local/bin/bwa
[09:01:59] Found bcftools - /usr/local/bin/bcftools
[09:01:59] Found samtools - /usr/local/bin/samtools
[09:01:59] Found java - /usr/local/bin/java
[09:01:59] Found snpEff - /usr/local/bin/snpEff
[09:01:59] Found samclip - /usr/local/bin/samclip
[09:01:59] Found seqtk - /usr/local/bin/seqtk
[09:01:59] Found parallel - /usr/local/bin/parallel
[09:01:59] Found freebayes - /usr/local/bin/freebayes
[09:01:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:01:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:01:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:01:59] Found vcfuniq - /usr/local/bin/vcfuniq
[09:01:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:01:59] Found gzip - /bin/gzip
[09:01:59] Found vt - /usr/local/bin/vt
[09:01:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:01:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:01:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:01:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:01:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:02:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:02:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:02:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:45:21] This is snippy 4.6.0Show full stderr[14:45:21] This is snippy 4.6.0
[14:45:21] Written by Torsten Seemann
[14:45:21] Obtained from https://github.com/tseemann/snippy
[14:45:21] Detected operating system: linux
[14:45:21] Enabling bundled linux tools.
[14:45:21] Found bwa - /usr/local/bin/bwa
[14:45:21] Found bcftools - /usr/local/bin/bcftools
[14:45:21] Found samtools - /usr/local/bin/samtools
[14:45:21] Found java - /usr/local/bin/java
[14:45:21] Found snpEff - /usr/local/bin/snpEff
[14:45:21] Found samclip - /usr/local/bin/samclip
[14:45:21] Found seqtk - /usr/local/bin/seqtk
[14:45:21] Found parallel - /usr/local/bin/parallel
[14:45:21] Found freebayes - /usr/local/bin/freebayes
[14:45:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:21] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:21] Found gzip - /bin/gzip
[14:45:21] Found vt - /usr/local/bin/vt
[14:45:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:45:27] This is snippy 4.6.0Show full stderr[14:45:27] This is snippy 4.6.0
[14:45:27] Written by Torsten Seemann
[14:45:27] Obtained from https://github.com/tseemann/snippy
[14:45:27] Detected operating system: linux
[14:45:27] Enabling bundled linux tools.
[14:45:27] Found bwa - /usr/local/bin/bwa
[14:45:27] Found bcftools - /usr/local/bin/bcftools
[14:45:27] Found samtools - /usr/local/bin/samtools
[14:45:27] Found java - /usr/local/bin/java
[14:45:27] Found snpEff - /usr/local/bin/snpEff
[14:45:27] Found samclip - /usr/local/bin/samclip
[14:45:27] Found seqtk - /usr/local/bin/seqtk
[14:45:27] Found parallel - /usr/local/bin/parallel
[14:45:27] Found freebayes - /usr/local/bin/freebayes
[14:45:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:27] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:27] Found gzip - /bin/gzip
[14:45:27] Found vt - /usr/local/bin/vt
[14:45:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:56:57] This is snippy 4.6.0Show full stderr[14:56:57] This is snippy 4.6.0
[14:56:57] Written by Torsten Seemann
[14:56:57] Obtained from https://github.com/tseemann/snippy
[14:56:57] Detected operating system: linux
[14:56:57] Enabling bundled linux tools.
[14:56:57] Found bwa - /usr/local/bin/bwa
[14:56:57] Found bcftools - /usr/local/bin/bcftools
[14:56:57] Found samtools - /usr/local/bin/samtools
[14:56:57] Found java - /usr/local/bin/java
[14:56:57] Found snpEff - /usr/local/bin/snpEff
[14:56:57] Found samclip - /usr/local/bin/samclip
[14:56:57] Found seqtk - /usr/local/bin/seqtk
[14:56:57] Found parallel - /usr/local/bin/parallel
[14:56:57] Found freebayes - /usr/local/bin/freebayes
[14:56:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:56:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:56:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:56:57] Found vcfuniq - /usr/local/bin/vcfuniq
[14:56:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:56:57] Found gzip - /bin/gzip
[14:56:57] Found vt - /usr/local/bin/vt
[14:56:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:56:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:56:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:56:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:56:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:56:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:56:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:56:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:03:55] This is snippy 4.6.0Show full stderr[15:03:55] This is snippy 4.6.0
[15:03:55] Written by Torsten Seemann
[15:03:55] Obtained from https://github.com/tseemann/snippy
[15:03:55] Detected operating system: linux
[15:03:55] Enabling bundled linux tools.
[15:03:55] Found bwa - /usr/local/bin/bwa
[15:03:55] Found bcftools - /usr/local/bin/bcftools
[15:03:55] Found samtools - /usr/local/bin/samtools
[15:03:55] Found java - /usr/local/bin/java
[15:03:55] Found snpEff - /usr/local/bin/snpEff
[15:03:55] Found samclip - /usr/local/bin/samclip
[15:03:55] Found seqtk - /usr/local/bin/seqtk
[15:03:55] Found parallel - /usr/local/bin/parallel
[15:03:55] Found freebayes - /usr/local/bin/freebayes
[15:03:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:03:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:03:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:03:55] Found vcfuniq - /usr/local/bin/vcfuniq
[15:03:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:03:55] Found gzip - /bin/gzip
[15:03:55] Found vt - /usr/local/bin/vt
[15:03:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:03:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:03:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:03:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:03:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:03:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:03:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:03:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:45:36] This is snippy 4.6.0Show full stderr[14:45:36] This is snippy 4.6.0
[14:45:36] Written by Torsten Seemann
[14:45:36] Obtained from https://github.com/tseemann/snippy
[14:45:36] Detected operating system: linux
[14:45:36] Enabling bundled linux tools.
[14:45:36] Found bwa - /usr/local/bin/bwa
[14:45:36] Found bcftools - /usr/local/bin/bcftools
[14:45:36] Found samtools - /usr/local/bin/samtools
[14:45:36] Found java - /usr/local/bin/java
[14:45:36] Found snpEff - /usr/local/bin/snpEff
[14:45:36] Found samclip - /usr/local/bin/samclip
[14:45:36] Found seqtk - /usr/local/bin/seqtk
[14:45:36] Found parallel - /usr/local/bin/parallel
[14:45:36] Found freebayes - /usr/local/bin/freebayes
[14:45:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:36] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:36] Found gzip - /bin/gzip
[14:45:36] Found vt - /usr/local/bin/vt
[14:45:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:45:42] This is snippy 4.6.0Show full stderr[14:45:42] This is snippy 4.6.0
[14:45:42] Written by Torsten Seemann
[14:45:42] Obtained from https://github.com/tseemann/snippy
[14:45:42] Detected operating system: linux
[14:45:42] Enabling bundled linux tools.
[14:45:42] Found bwa - /usr/local/bin/bwa
[14:45:42] Found bcftools - /usr/local/bin/bcftools
[14:45:42] Found samtools - /usr/local/bin/samtools
[14:45:42] Found java - /usr/local/bin/java
[14:45:42] Found snpEff - /usr/local/bin/snpEff
[14:45:42] Found samclip - /usr/local/bin/samclip
[14:45:42] Found seqtk - /usr/local/bin/seqtk
[14:45:42] Found parallel - /usr/local/bin/parallel
[14:45:42] Found freebayes - /usr/local/bin/freebayes
[14:45:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:45:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:45:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:45:42] Found vcfuniq - /usr/local/bin/vcfuniq
[14:45:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:45:42] Found gzip - /bin/gzip
[14:45:42] Found vt - /usr/local/bin/vt
[14:45:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:45:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:45:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:45:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:45:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:45:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:45:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:45:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:46:04] This is snippy 4.6.0Show full stderr[14:46:04] This is snippy 4.6.0
[14:46:04] Written by Torsten Seemann
[14:46:04] Obtained from https://github.com/tseemann/snippy
[14:46:04] Detected operating system: linux
[14:46:04] Enabling bundled linux tools.
[14:46:04] Found bwa - /usr/local/bin/bwa
[14:46:04] Found bcftools - /usr/local/bin/bcftools
[14:46:04] Found samtools - /usr/local/bin/samtools
[14:46:04] Found java - /usr/local/bin/java
[14:46:04] Found snpEff - /usr/local/bin/snpEff
[14:46:04] Found samclip - /usr/local/bin/samclip
[14:46:04] Found seqtk - /usr/local/bin/seqtk
[14:46:04] Found parallel - /usr/local/bin/parallel
[14:46:04] Found freebayes - /usr/local/bin/freebayes
[14:46:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:04] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:04] Found gzip - /bin/gzip
[14:46:04] Found vt - /usr/local/bin/vt
[14:46:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:46:00] This is snippy 4.6.0Show full stderr[14:46:00] This is snippy 4.6.0
[14:46:00] Written by Torsten Seemann
[14:46:00] Obtained from https://github.com/tseemann/snippy
[14:46:00] Detected operating system: linux
[14:46:00] Enabling bundled linux tools.
[14:46:00] Found bwa - /usr/local/bin/bwa
[14:46:00] Found bcftools - /usr/local/bin/bcftools
[14:46:00] Found samtools - /usr/local/bin/samtools
[14:46:00] Found java - /usr/local/bin/java
[14:46:00] Found snpEff - /usr/local/bin/snpEff
[14:46:00] Found samclip - /usr/local/bin/samclip
[14:46:00] Found seqtk - /usr/local/bin/seqtk
[14:46:00] Found parallel - /usr/local/bin/parallel
[14:46:00] Found freebayes - /usr/local/bin/freebayes
[14:46:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:00] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:00] Found gzip - /bin/gzip
[14:46:00] Found vt - /usr/local/bin/vt
[14:46:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:46:22] This is snippy 4.6.0Show full stderr[14:46:22] This is snippy 4.6.0
[14:46:22] Written by Torsten Seemann
[14:46:22] Obtained from https://github.com/tseemann/snippy
[14:46:22] Detected operating system: linux
[14:46:22] Enabling bundled linux tools.
[14:46:22] Found bwa - /usr/local/bin/bwa
[14:46:22] Found bcftools - /usr/local/bin/bcftools
[14:46:22] Found samtools - /usr/local/bin/samtools
[14:46:22] Found java - /usr/local/bin/java
[14:46:22] Found snpEff - /usr/local/bin/snpEff
[14:46:22] Found samclip - /usr/local/bin/samclip
[14:46:22] Found seqtk - /usr/local/bin/seqtk
[14:46:22] Found parallel - /usr/local/bin/parallel
[14:46:22] Found freebayes - /usr/local/bin/freebayes
[14:46:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:22] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:22] Found gzip - /bin/gzip
[14:46:22] Found vt - /usr/local/bin/vt
[14:46:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:09:00] This is snippy 4.6.0Show full stderr[15:09:00] This is snippy 4.6.0
[15:09:00] Written by Torsten Seemann
[15:09:00] Obtained from https://github.com/tseemann/snippy
[15:09:00] Detected operating system: linux
[15:09:00] Enabling bundled linux tools.
[15:09:00] Found bwa - /usr/local/bin/bwa
[15:09:00] Found bcftools - /usr/local/bin/bcftools
[15:09:00] Found samtools - /usr/local/bin/samtools
[15:09:00] Found java - /usr/local/bin/java
[15:09:00] Found snpEff - /usr/local/bin/snpEff
[15:09:00] Found samclip - /usr/local/bin/samclip
[15:09:00] Found seqtk - /usr/local/bin/seqtk
[15:09:00] Found parallel - /usr/local/bin/parallel
[15:09:00] Found freebayes - /usr/local/bin/freebayes
[15:09:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:09:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:09:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:09:00] Found vcfuniq - /usr/local/bin/vcfuniq
[15:09:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:09:00] Found gzip - /bin/gzip
[15:09:00] Found vt - /usr/local/bin/vt
[15:09:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:09:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:09:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:09:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:09:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:09:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:09:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:09:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:14:53] This is snippy 4.6.0Show full stderr[15:14:53] This is snippy 4.6.0
[15:14:53] Written by Torsten Seemann
[15:14:53] Obtained from https://github.com/tseemann/snippy
[15:14:53] Detected operating system: linux
[15:14:53] Enabling bundled linux tools.
[15:14:53] Found bwa - /usr/local/bin/bwa
[15:14:53] Found bcftools - /usr/local/bin/bcftools
[15:14:53] Found samtools - /usr/local/bin/samtools
[15:14:53] Found java - /usr/local/bin/java
[15:14:53] Found snpEff - /usr/local/bin/snpEff
[15:14:53] Found samclip - /usr/local/bin/samclip
[15:14:53] Found seqtk - /usr/local/bin/seqtk
[15:14:53] Found parallel - /usr/local/bin/parallel
[15:14:53] Found freebayes - /usr/local/bin/freebayes
[15:14:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:14:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:14:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:14:53] Found vcfuniq - /usr/local/bin/vcfuniq
[15:14:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:14:53] Found gzip - /bin/gzip
[15:14:53] Found vt - /usr/local/bin/vt
[15:14:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:14:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:14:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:14:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:14:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:14:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:14:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:14:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:20:59] This is snippy 4.6.0Show full stderr[15:20:59] This is snippy 4.6.0
[15:20:59] Written by Torsten Seemann
[15:20:59] Obtained from https://github.com/tseemann/snippy
[15:20:59] Detected operating system: linux
[15:20:59] Enabling bundled linux tools.
[15:20:59] Found bwa - /usr/local/bin/bwa
[15:20:59] Found bcftools - /usr/local/bin/bcftools
[15:20:59] Found samtools - /usr/local/bin/samtools
[15:20:59] Found java - /usr/local/bin/java
[15:20:59] Found snpEff - /usr/local/bin/snpEff
[15:20:59] Found samclip - /usr/local/bin/samclip
[15:20:59] Found seqtk - /usr/local/bin/seqtk
[15:20:59] Found parallel - /usr/local/bin/parallel
[15:20:59] Found freebayes - /usr/local/bin/freebayes
[15:20:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:20:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:20:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:20:59] Found vcfuniq - /usr/local/bin/vcfuniq
[15:20:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:20:59] Found gzip - /bin/gzip
[15:20:59] Found vt - /usr/local/bin/vt
[15:20:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:20:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:20:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:20:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:20:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:21:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:21:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:21:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:46:06] This is snippy 4.6.0Show full stderr[14:46:06] This is snippy 4.6.0
[14:46:06] Written by Torsten Seemann
[14:46:06] Obtained from https://github.com/tseemann/snippy
[14:46:06] Detected operating system: linux
[14:46:06] Enabling bundled linux tools.
[14:46:06] Found bwa - /usr/local/bin/bwa
[14:46:06] Found bcftools - /usr/local/bin/bcftools
[14:46:06] Found samtools - /usr/local/bin/samtools
[14:46:06] Found java - /usr/local/bin/java
[14:46:06] Found snpEff - /usr/local/bin/snpEff
[14:46:06] Found samclip - /usr/local/bin/samclip
[14:46:06] Found seqtk - /usr/local/bin/seqtk
[14:46:06] Found parallel - /usr/local/bin/parallel
[14:46:06] Found freebayes - /usr/local/bin/freebayes
[14:46:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:06] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:06] Found gzip - /bin/gzip
[14:46:06] Found vt - /usr/local/bin/vt
[14:46:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:58:21] This is snippy 4.6.0Show full stderr[14:58:21] This is snippy 4.6.0
[14:58:21] Written by Torsten Seemann
[14:58:21] Obtained from https://github.com/tseemann/snippy
[14:58:21] Detected operating system: linux
[14:58:21] Enabling bundled linux tools.
[14:58:21] Found bwa - /usr/local/bin/bwa
[14:58:21] Found bcftools - /usr/local/bin/bcftools
[14:58:21] Found samtools - /usr/local/bin/samtools
[14:58:21] Found java - /usr/local/bin/java
[14:58:21] Found snpEff - /usr/local/bin/snpEff
[14:58:21] Found samclip - /usr/local/bin/samclip
[14:58:21] Found seqtk - /usr/local/bin/seqtk
[14:58:21] Found parallel - /usr/local/bin/parallel
[14:58:21] Found freebayes - /usr/local/bin/freebayes
[14:58:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:58:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:58:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:58:21] Found vcfuniq - /usr/local/bin/vcfuniq
[14:58:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:58:21] Found gzip - /bin/gzip
[14:58:21] Found vt - /usr/local/bin/vt
[14:58:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:58:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:58:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:58:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:58:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:58:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:58:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:58:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:04:25] This is snippy 4.6.0Show full stderr[15:04:25] This is snippy 4.6.0
[15:04:25] Written by Torsten Seemann
[15:04:25] Obtained from https://github.com/tseemann/snippy
[15:04:25] Detected operating system: linux
[15:04:25] Enabling bundled linux tools.
[15:04:25] Found bwa - /usr/local/bin/bwa
[15:04:25] Found bcftools - /usr/local/bin/bcftools
[15:04:25] Found samtools - /usr/local/bin/samtools
[15:04:25] Found java - /usr/local/bin/java
[15:04:25] Found snpEff - /usr/local/bin/snpEff
[15:04:25] Found samclip - /usr/local/bin/samclip
[15:04:25] Found seqtk - /usr/local/bin/seqtk
[15:04:25] Found parallel - /usr/local/bin/parallel
[15:04:25] Found freebayes - /usr/local/bin/freebayes
[15:04:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:04:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:04:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:04:25] Found vcfuniq - /usr/local/bin/vcfuniq
[15:04:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:04:25] Found gzip - /bin/gzip
[15:04:25] Found vt - /usr/local/bin/vt
[15:04:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:04:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:04:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:04:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:04:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:04:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:04:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:04:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:49:18] This is snippy 4.6.0Show full stderr[14:49:18] This is snippy 4.6.0
[14:49:18] Written by Torsten Seemann
[14:49:18] Obtained from https://github.com/tseemann/snippy
[14:49:18] Detected operating system: linux
[14:49:18] Enabling bundled linux tools.
[14:49:18] Found bwa - /usr/local/bin/bwa
[14:49:18] Found bcftools - /usr/local/bin/bcftools
[14:49:18] Found samtools - /usr/local/bin/samtools
[14:49:18] Found java - /usr/local/bin/java
[14:49:18] Found snpEff - /usr/local/bin/snpEff
[14:49:18] Found samclip - /usr/local/bin/samclip
[14:49:18] Found seqtk - /usr/local/bin/seqtk
[14:49:18] Found parallel - /usr/local/bin/parallel
[14:49:18] Found freebayes - /usr/local/bin/freebayes
[14:49:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:18] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:18] Found gzip - /bin/gzip
[14:49:18] Found vt - /usr/local/bin/vt
[14:49:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:46:15] This is snippy 4.6.0Show full stderr[14:46:15] This is snippy 4.6.0
[14:46:15] Written by Torsten Seemann
[14:46:15] Obtained from https://github.com/tseemann/snippy
[14:46:15] Detected operating system: linux
[14:46:15] Enabling bundled linux tools.
[14:46:15] Found bwa - /usr/local/bin/bwa
[14:46:15] Found bcftools - /usr/local/bin/bcftools
[14:46:15] Found samtools - /usr/local/bin/samtools
[14:46:15] Found java - /usr/local/bin/java
[14:46:15] Found snpEff - /usr/local/bin/snpEff
[14:46:15] Found samclip - /usr/local/bin/samclip
[14:46:15] Found seqtk - /usr/local/bin/seqtk
[14:46:15] Found parallel - /usr/local/bin/parallel
[14:46:15] Found freebayes - /usr/local/bin/freebayes
[14:46:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:15] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:15] Found gzip - /bin/gzip
[14:46:15] Found vt - /usr/local/bin/vt
[14:46:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:46:40] This is snippy 4.6.0Show full stderr[14:46:40] This is snippy 4.6.0
[14:46:40] Written by Torsten Seemann
[14:46:40] Obtained from https://github.com/tseemann/snippy
[14:46:40] Detected operating system: linux
[14:46:40] Enabling bundled linux tools.
[14:46:40] Found bwa - /usr/local/bin/bwa
[14:46:40] Found bcftools - /usr/local/bin/bcftools
[14:46:40] Found samtools - /usr/local/bin/samtools
[14:46:40] Found java - /usr/local/bin/java
[14:46:40] Found snpEff - /usr/local/bin/snpEff
[14:46:40] Found samclip - /usr/local/bin/samclip
[14:46:40] Found seqtk - /usr/local/bin/seqtk
[14:46:40] Found parallel - /usr/local/bin/parallel
[14:46:40] Found freebayes - /usr/local/bin/freebayes
[14:46:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:46:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:46:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:46:40] Found vcfuniq - /usr/local/bin/vcfuniq
[14:46:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:46:40] Found gzip - /bin/gzip
[14:46:40] Found vt - /usr/local/bin/vt
[14:46:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:46:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:46:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:46:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:46:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:46:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:46:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:46:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:47:56] This is snippy 4.6.0Show full stderr[14:47:56] This is snippy 4.6.0
[14:47:56] Written by Torsten Seemann
[14:47:56] Obtained from https://github.com/tseemann/snippy
[14:47:56] Detected operating system: linux
[14:47:56] Enabling bundled linux tools.
[14:47:56] Found bwa - /usr/local/bin/bwa
[14:47:56] Found bcftools - /usr/local/bin/bcftools
[14:47:56] Found samtools - /usr/local/bin/samtools
[14:47:56] Found java - /usr/local/bin/java
[14:47:56] Found snpEff - /usr/local/bin/snpEff
[14:47:56] Found samclip - /usr/local/bin/samclip
[14:47:56] Found seqtk - /usr/local/bin/seqtk
[14:47:56] Found parallel - /usr/local/bin/parallel
[14:47:56] Found freebayes - /usr/local/bin/freebayes
[14:47:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:47:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:47:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:47:56] Found vcfuniq - /usr/local/bin/vcfuniq
[14:47:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:47:56] Found gzip - /bin/gzip
[14:47:56] Found vt - /usr/local/bin/vt
[14:47:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:47:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:47:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:47:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:47:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:47:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:47:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:47:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:48:12] This is snippy 4.6.0Show full stderr[14:48:12] This is snippy 4.6.0
[14:48:12] Written by Torsten Seemann
[14:48:12] Obtained from https://github.com/tseemann/snippy
[14:48:12] Detected operating system: linux
[14:48:12] Enabling bundled linux tools.
[14:48:12] Found bwa - /usr/local/bin/bwa
[14:48:12] Found bcftools - /usr/local/bin/bcftools
[14:48:12] Found samtools - /usr/local/bin/samtools
[14:48:12] Found java - /usr/local/bin/java
[14:48:12] Found snpEff - /usr/local/bin/snpEff
[14:48:12] Found samclip - /usr/local/bin/samclip
[14:48:12] Found seqtk - /usr/local/bin/seqtk
[14:48:12] Found parallel - /usr/local/bin/parallel
[14:48:12] Found freebayes - /usr/local/bin/freebayes
[14:48:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:12] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:12] Found gzip - /bin/gzip
[14:48:12] Found vt - /usr/local/bin/vt
[14:48:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:48:15] This is snippy 4.6.0Show full stderr[14:48:15] This is snippy 4.6.0
[14:48:15] Written by Torsten Seemann
[14:48:15] Obtained from https://github.com/tseemann/snippy
[14:48:15] Detected operating system: linux
[14:48:15] Enabling bundled linux tools.
[14:48:15] Found bwa - /usr/local/bin/bwa
[14:48:15] Found bcftools - /usr/local/bin/bcftools
[14:48:15] Found samtools - /usr/local/bin/samtools
[14:48:15] Found java - /usr/local/bin/java
[14:48:15] Found snpEff - /usr/local/bin/snpEff
[14:48:15] Found samclip - /usr/local/bin/samclip
[14:48:15] Found seqtk - /usr/local/bin/seqtk
[14:48:15] Found parallel - /usr/local/bin/parallel
[14:48:15] Found freebayes - /usr/local/bin/freebayes
[14:48:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:15] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:15] Found gzip - /bin/gzip
[14:48:15] Found vt - /usr/local/bin/vt
[14:48:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:48:27] This is snippy 4.6.0Show full stderr[14:48:27] This is snippy 4.6.0
[14:48:27] Written by Torsten Seemann
[14:48:27] Obtained from https://github.com/tseemann/snippy
[14:48:27] Detected operating system: linux
[14:48:27] Enabling bundled linux tools.
[14:48:27] Found bwa - /usr/local/bin/bwa
[14:48:27] Found bcftools - /usr/local/bin/bcftools
[14:48:27] Found samtools - /usr/local/bin/samtools
[14:48:27] Found java - /usr/local/bin/java
[14:48:27] Found snpEff - /usr/local/bin/snpEff
[14:48:27] Found samclip - /usr/local/bin/samclip
[14:48:27] Found seqtk - /usr/local/bin/seqtk
[14:48:27] Found parallel - /usr/local/bin/parallel
[14:48:27] Found freebayes - /usr/local/bin/freebayes
[14:48:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:27] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:27] Found gzip - /bin/gzip
[14:48:27] Found vt - /usr/local/bin/vt
[14:48:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:48:51] This is snippy 4.6.0Show full stderr[14:48:51] This is snippy 4.6.0
[14:48:51] Written by Torsten Seemann
[14:48:51] Obtained from https://github.com/tseemann/snippy
[14:48:51] Detected operating system: linux
[14:48:51] Enabling bundled linux tools.
[14:48:51] Found bwa - /usr/local/bin/bwa
[14:48:51] Found bcftools - /usr/local/bin/bcftools
[14:48:51] Found samtools - /usr/local/bin/samtools
[14:48:51] Found java - /usr/local/bin/java
[14:48:51] Found snpEff - /usr/local/bin/snpEff
[14:48:51] Found samclip - /usr/local/bin/samclip
[14:48:51] Found seqtk - /usr/local/bin/seqtk
[14:48:51] Found parallel - /usr/local/bin/parallel
[14:48:51] Found freebayes - /usr/local/bin/freebayes
[14:48:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:51] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:51] Found gzip - /bin/gzip
[14:48:51] Found vt - /usr/local/bin/vt
[14:48:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:47:40] This is snippy 4.6.0Show full stderr[14:47:40] This is snippy 4.6.0
[14:47:40] Written by Torsten Seemann
[14:47:40] Obtained from https://github.com/tseemann/snippy
[14:47:40] Detected operating system: linux
[14:47:40] Enabling bundled linux tools.
[14:47:40] Found bwa - /usr/local/bin/bwa
[14:47:40] Found bcftools - /usr/local/bin/bcftools
[14:47:40] Found samtools - /usr/local/bin/samtools
[14:47:40] Found java - /usr/local/bin/java
[14:47:40] Found snpEff - /usr/local/bin/snpEff
[14:47:40] Found samclip - /usr/local/bin/samclip
[14:47:40] Found seqtk - /usr/local/bin/seqtk
[14:47:40] Found parallel - /usr/local/bin/parallel
[14:47:40] Found freebayes - /usr/local/bin/freebayes
[14:47:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:47:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:47:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:47:40] Found vcfuniq - /usr/local/bin/vcfuniq
[14:47:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:47:40] Found gzip - /bin/gzip
[14:47:40] Found vt - /usr/local/bin/vt
[14:47:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:47:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:47:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:47:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:47:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:47:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:47:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:47:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:47:54] This is snippy 4.6.0Show full stderr[14:47:54] This is snippy 4.6.0
[14:47:54] Written by Torsten Seemann
[14:47:54] Obtained from https://github.com/tseemann/snippy
[14:47:54] Detected operating system: linux
[14:47:54] Enabling bundled linux tools.
[14:47:54] Found bwa - /usr/local/bin/bwa
[14:47:54] Found bcftools - /usr/local/bin/bcftools
[14:47:54] Found samtools - /usr/local/bin/samtools
[14:47:54] Found java - /usr/local/bin/java
[14:47:54] Found snpEff - /usr/local/bin/snpEff
[14:47:54] Found samclip - /usr/local/bin/samclip
[14:47:54] Found seqtk - /usr/local/bin/seqtk
[14:47:54] Found parallel - /usr/local/bin/parallel
[14:47:54] Found freebayes - /usr/local/bin/freebayes
[14:47:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:47:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:47:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:47:54] Found vcfuniq - /usr/local/bin/vcfuniq
[14:47:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:47:54] Found gzip - /bin/gzip
[14:47:54] Found vt - /usr/local/bin/vt
[14:47:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:47:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:47:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:47:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:47:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:47:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:47:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:47:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:48:30] This is snippy 4.6.0Show full stderr[14:48:30] This is snippy 4.6.0
[14:48:30] Written by Torsten Seemann
[14:48:30] Obtained from https://github.com/tseemann/snippy
[14:48:30] Detected operating system: linux
[14:48:30] Enabling bundled linux tools.
[14:48:30] Found bwa - /usr/local/bin/bwa
[14:48:30] Found bcftools - /usr/local/bin/bcftools
[14:48:30] Found samtools - /usr/local/bin/samtools
[14:48:30] Found java - /usr/local/bin/java
[14:48:30] Found snpEff - /usr/local/bin/snpEff
[14:48:30] Found samclip - /usr/local/bin/samclip
[14:48:30] Found seqtk - /usr/local/bin/seqtk
[14:48:30] Found parallel - /usr/local/bin/parallel
[14:48:30] Found freebayes - /usr/local/bin/freebayes
[14:48:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:30] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:30] Found gzip - /bin/gzip
[14:48:30] Found vt - /usr/local/bin/vt
[14:48:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:48:33] This is snippy 4.6.0Show full stderr[14:48:33] This is snippy 4.6.0
[14:48:33] Written by Torsten Seemann
[14:48:33] Obtained from https://github.com/tseemann/snippy
[14:48:33] Detected operating system: linux
[14:48:33] Enabling bundled linux tools.
[14:48:33] Found bwa - /usr/local/bin/bwa
[14:48:33] Found bcftools - /usr/local/bin/bcftools
[14:48:33] Found samtools - /usr/local/bin/samtools
[14:48:33] Found java - /usr/local/bin/java
[14:48:33] Found snpEff - /usr/local/bin/snpEff
[14:48:33] Found samclip - /usr/local/bin/samclip
[14:48:33] Found seqtk - /usr/local/bin/seqtk
[14:48:33] Found parallel - /usr/local/bin/parallel
[14:48:33] Found freebayes - /usr/local/bin/freebayes
[14:48:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:33] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:33] Found gzip - /bin/gzip
[14:48:33] Found vt - /usr/local/bin/vt
[14:48:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:49:00] This is snippy 4.6.0Show full stderr[14:49:00] This is snippy 4.6.0
[14:49:00] Written by Torsten Seemann
[14:49:00] Obtained from https://github.com/tseemann/snippy
[14:49:00] Detected operating system: linux
[14:49:00] Enabling bundled linux tools.
[14:49:00] Found bwa - /usr/local/bin/bwa
[14:49:00] Found bcftools - /usr/local/bin/bcftools
[14:49:00] Found samtools - /usr/local/bin/samtools
[14:49:00] Found java - /usr/local/bin/java
[14:49:00] Found snpEff - /usr/local/bin/snpEff
[14:49:00] Found samclip - /usr/local/bin/samclip
[14:49:00] Found seqtk - /usr/local/bin/seqtk
[14:49:00] Found parallel - /usr/local/bin/parallel
[14:49:00] Found freebayes - /usr/local/bin/freebayes
[14:49:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:00] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:00] Found gzip - /bin/gzip
[14:49:00] Found vt - /usr/local/bin/vt
[14:49:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:49:04] This is snippy 4.6.0Show full stderr[14:49:04] This is snippy 4.6.0
[14:49:04] Written by Torsten Seemann
[14:49:04] Obtained from https://github.com/tseemann/snippy
[14:49:04] Detected operating system: linux
[14:49:04] Enabling bundled linux tools.
[14:49:04] Found bwa - /usr/local/bin/bwa
[14:49:04] Found bcftools - /usr/local/bin/bcftools
[14:49:04] Found samtools - /usr/local/bin/samtools
[14:49:04] Found java - /usr/local/bin/java
[14:49:04] Found snpEff - /usr/local/bin/snpEff
[14:49:04] Found samclip - /usr/local/bin/samclip
[14:49:04] Found seqtk - /usr/local/bin/seqtk
[14:49:04] Found parallel - /usr/local/bin/parallel
[14:49:04] Found freebayes - /usr/local/bin/freebayes
[14:49:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:04] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:04] Found gzip - /bin/gzip
[14:49:04] Found vt - /usr/local/bin/vt
[14:49:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:49:14] This is snippy 4.6.0Show full stderr[14:49:14] This is snippy 4.6.0
[14:49:14] Written by Torsten Seemann
[14:49:14] Obtained from https://github.com/tseemann/snippy
[14:49:14] Detected operating system: linux
[14:49:14] Enabling bundled linux tools.
[14:49:14] Found bwa - /usr/local/bin/bwa
[14:49:14] Found bcftools - /usr/local/bin/bcftools
[14:49:14] Found samtools - /usr/local/bin/samtools
[14:49:14] Found java - /usr/local/bin/java
[14:49:14] Found snpEff - /usr/local/bin/snpEff
[14:49:14] Found samclip - /usr/local/bin/samclip
[14:49:14] Found seqtk - /usr/local/bin/seqtk
[14:49:14] Found parallel - /usr/local/bin/parallel
[14:49:14] Found freebayes - /usr/local/bin/freebayes
[14:49:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:14] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:14] Found gzip - /bin/gzip
[14:49:14] Found vt - /usr/local/bin/vt
[14:49:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:48:06] This is snippy 4.6.0Show full stderr[14:48:06] This is snippy 4.6.0
[14:48:06] Written by Torsten Seemann
[14:48:06] Obtained from https://github.com/tseemann/snippy
[14:48:06] Detected operating system: linux
[14:48:06] Enabling bundled linux tools.
[14:48:06] Found bwa - /usr/local/bin/bwa
[14:48:06] Found bcftools - /usr/local/bin/bcftools
[14:48:06] Found samtools - /usr/local/bin/samtools
[14:48:06] Found java - /usr/local/bin/java
[14:48:06] Found snpEff - /usr/local/bin/snpEff
[14:48:06] Found samclip - /usr/local/bin/samclip
[14:48:06] Found seqtk - /usr/local/bin/seqtk
[14:48:06] Found parallel - /usr/local/bin/parallel
[14:48:06] Found freebayes - /usr/local/bin/freebayes
[14:48:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:06] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:06] Found gzip - /bin/gzip
[14:48:06] Found vt - /usr/local/bin/vt
[14:48:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:48:18] This is snippy 4.6.0Show full stderr[14:48:18] This is snippy 4.6.0
[14:48:18] Written by Torsten Seemann
[14:48:18] Obtained from https://github.com/tseemann/snippy
[14:48:18] Detected operating system: linux
[14:48:18] Enabling bundled linux tools.
[14:48:18] Found bwa - /usr/local/bin/bwa
[14:48:18] Found bcftools - /usr/local/bin/bcftools
[14:48:18] Found samtools - /usr/local/bin/samtools
[14:48:18] Found java - /usr/local/bin/java
[14:48:18] Found snpEff - /usr/local/bin/snpEff
[14:48:18] Found samclip - /usr/local/bin/samclip
[14:48:18] Found seqtk - /usr/local/bin/seqtk
[14:48:18] Found parallel - /usr/local/bin/parallel
[14:48:18] Found freebayes - /usr/local/bin/freebayes
[14:48:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:18] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:18] Found gzip - /bin/gzip
[14:48:18] Found vt - /usr/local/bin/vt
[14:48:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:48:21] This is snippy 4.6.0Show full stderr[14:48:21] This is snippy 4.6.0
[14:48:21] Written by Torsten Seemann
[14:48:21] Obtained from https://github.com/tseemann/snippy
[14:48:21] Detected operating system: linux
[14:48:21] Enabling bundled linux tools.
[14:48:21] Found bwa - /usr/local/bin/bwa
[14:48:21] Found bcftools - /usr/local/bin/bcftools
[14:48:21] Found samtools - /usr/local/bin/samtools
[14:48:21] Found java - /usr/local/bin/java
[14:48:21] Found snpEff - /usr/local/bin/snpEff
[14:48:21] Found samclip - /usr/local/bin/samclip
[14:48:21] Found seqtk - /usr/local/bin/seqtk
[14:48:21] Found parallel - /usr/local/bin/parallel
[14:48:21] Found freebayes - /usr/local/bin/freebayes
[14:48:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:21] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:21] Found gzip - /bin/gzip
[14:48:21] Found vt - /usr/local/bin/vt
[14:48:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:48:36] This is snippy 4.6.0Show full stderr[14:48:36] This is snippy 4.6.0
[14:48:36] Written by Torsten Seemann
[14:48:36] Obtained from https://github.com/tseemann/snippy
[14:48:36] Detected operating system: linux
[14:48:36] Enabling bundled linux tools.
[14:48:36] Found bwa - /usr/local/bin/bwa
[14:48:36] Found bcftools - /usr/local/bin/bcftools
[14:48:36] Found samtools - /usr/local/bin/samtools
[14:48:37] Found java - /usr/local/bin/java
[14:48:37] Found snpEff - /usr/local/bin/snpEff
[14:48:37] Found samclip - /usr/local/bin/samclip
[14:48:37] Found seqtk - /usr/local/bin/seqtk
[14:48:37] Found parallel - /usr/local/bin/parallel
[14:48:37] Found freebayes - /usr/local/bin/freebayes
[14:48:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:37] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:37] Found gzip - /bin/gzip
[14:48:37] Found vt - /usr/local/bin/vt
[14:48:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:48:48] This is snippy 4.6.0Show full stderr[14:48:48] This is snippy 4.6.0
[14:48:48] Written by Torsten Seemann
[14:48:48] Obtained from https://github.com/tseemann/snippy
[14:48:48] Detected operating system: linux
[14:48:48] Enabling bundled linux tools.
[14:48:48] Found bwa - /usr/local/bin/bwa
[14:48:48] Found bcftools - /usr/local/bin/bcftools
[14:48:48] Found samtools - /usr/local/bin/samtools
[14:48:48] Found java - /usr/local/bin/java
[14:48:49] Found snpEff - /usr/local/bin/snpEff
[14:48:49] Found samclip - /usr/local/bin/samclip
[14:48:49] Found seqtk - /usr/local/bin/seqtk
[14:48:49] Found parallel - /usr/local/bin/parallel
[14:48:49] Found freebayes - /usr/local/bin/freebayes
[14:48:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:48:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:48:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:48:49] Found vcfuniq - /usr/local/bin/vcfuniq
[14:48:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:48:49] Found gzip - /bin/gzip
[14:48:49] Found vt - /usr/local/bin/vt
[14:48:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:48:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:48:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:48:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:48:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:48:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:48:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:48:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:49:29] This is snippy 4.6.0Show full stderr[14:49:29] This is snippy 4.6.0
[14:49:29] Written by Torsten Seemann
[14:49:29] Obtained from https://github.com/tseemann/snippy
[14:49:29] Detected operating system: linux
[14:49:29] Enabling bundled linux tools.
[14:49:29] Found bwa - /usr/local/bin/bwa
[14:49:29] Found bcftools - /usr/local/bin/bcftools
[14:49:29] Found samtools - /usr/local/bin/samtools
[14:49:30] Found java - /usr/local/bin/java
[14:49:30] Found snpEff - /usr/local/bin/snpEff
[14:49:30] Found samclip - /usr/local/bin/samclip
[14:49:30] Found seqtk - /usr/local/bin/seqtk
[14:49:30] Found parallel - /usr/local/bin/parallel
[14:49:30] Found freebayes - /usr/local/bin/freebayes
[14:49:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:30] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:30] Found gzip - /bin/gzip
[14:49:30] Found vt - /usr/local/bin/vt
[14:49:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:26] This is snippy 4.6.0Show full stderr[14:50:26] This is snippy 4.6.0
[14:50:26] Written by Torsten Seemann
[14:50:26] Obtained from https://github.com/tseemann/snippy
[14:50:26] Detected operating system: linux
[14:50:26] Enabling bundled linux tools.
[14:50:26] Found bwa - /usr/local/bin/bwa
[14:50:26] Found bcftools - /usr/local/bin/bcftools
[14:50:26] Found samtools - /usr/local/bin/samtools
[14:50:26] Found java - /usr/local/bin/java
[14:50:26] Found snpEff - /usr/local/bin/snpEff
[14:50:26] Found samclip - /usr/local/bin/samclip
[14:50:26] Found seqtk - /usr/local/bin/seqtk
[14:50:26] Found parallel - /usr/local/bin/parallel
[14:50:26] Found freebayes - /usr/local/bin/freebayes
[14:50:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:27] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:27] Found gzip - /bin/gzip
[14:50:27] Found vt - /usr/local/bin/vt
[14:50:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:51] This is snippy 4.6.0Show full stderr[14:50:51] This is snippy 4.6.0
[14:50:51] Written by Torsten Seemann
[14:50:51] Obtained from https://github.com/tseemann/snippy
[14:50:51] Detected operating system: linux
[14:50:51] Enabling bundled linux tools.
[14:50:51] Found bwa - /usr/local/bin/bwa
[14:50:51] Found bcftools - /usr/local/bin/bcftools
[14:50:51] Found samtools - /usr/local/bin/samtools
[14:50:51] Found java - /usr/local/bin/java
[14:50:51] Found snpEff - /usr/local/bin/snpEff
[14:50:51] Found samclip - /usr/local/bin/samclip
[14:50:51] Found seqtk - /usr/local/bin/seqtk
[14:50:51] Found parallel - /usr/local/bin/parallel
[14:50:51] Found freebayes - /usr/local/bin/freebayes
[14:50:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:51] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:51] Found gzip - /bin/gzip
[14:50:51] Found vt - /usr/local/bin/vt
[14:50:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:51:09] This is snippy 4.6.0Show full stderr[14:51:09] This is snippy 4.6.0
[14:51:09] Written by Torsten Seemann
[14:51:09] Obtained from https://github.com/tseemann/snippy
[14:51:09] Detected operating system: linux
[14:51:09] Enabling bundled linux tools.
[14:51:09] Found bwa - /usr/local/bin/bwa
[14:51:09] Found bcftools - /usr/local/bin/bcftools
[14:51:09] Found samtools - /usr/local/bin/samtools
[14:51:09] Found java - /usr/local/bin/java
[14:51:09] Found snpEff - /usr/local/bin/snpEff
[14:51:09] Found samclip - /usr/local/bin/samclip
[14:51:09] Found seqtk - /usr/local/bin/seqtk
[14:51:09] Found parallel - /usr/local/bin/parallel
[14:51:09] Found freebayes - /usr/local/bin/freebayes
[14:51:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:09] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:09] Found gzip - /bin/gzip
[14:51:09] Found vt - /usr/local/bin/vt
[14:51:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:51:10] This is snippy 4.6.0Show full stderr[14:51:10] This is snippy 4.6.0
[14:51:10] Written by Torsten Seemann
[14:51:10] Obtained from https://github.com/tseemann/snippy
[14:51:10] Detected operating system: linux
[14:51:10] Enabling bundled linux tools.
[14:51:10] Found bwa - /usr/local/bin/bwa
[14:51:10] Found bcftools - /usr/local/bin/bcftools
[14:51:10] Found samtools - /usr/local/bin/samtools
[14:51:10] Found java - /usr/local/bin/java
[14:51:10] Found snpEff - /usr/local/bin/snpEff
[14:51:10] Found samclip - /usr/local/bin/samclip
[14:51:10] Found seqtk - /usr/local/bin/seqtk
[14:51:10] Found parallel - /usr/local/bin/parallel
[14:51:10] Found freebayes - /usr/local/bin/freebayes
[14:51:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:10] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:10] Found gzip - /bin/gzip
[14:51:10] Found vt - /usr/local/bin/vt
[14:51:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:51:28] This is snippy 4.6.0Show full stderr[14:51:28] This is snippy 4.6.0
[14:51:28] Written by Torsten Seemann
[14:51:28] Obtained from https://github.com/tseemann/snippy
[14:51:28] Detected operating system: linux
[14:51:28] Enabling bundled linux tools.
[14:51:28] Found bwa - /usr/local/bin/bwa
[14:51:28] Found bcftools - /usr/local/bin/bcftools
[14:51:29] Found samtools - /usr/local/bin/samtools
[14:51:29] Found java - /usr/local/bin/java
[14:51:29] Found snpEff - /usr/local/bin/snpEff
[14:51:29] Found samclip - /usr/local/bin/samclip
[14:51:29] Found seqtk - /usr/local/bin/seqtk
[14:51:29] Found parallel - /usr/local/bin/parallel
[14:51:29] Found freebayes - /usr/local/bin/freebayes
[14:51:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:29] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:29] Found gzip - /bin/gzip
[14:51:29] Found vt - /usr/local/bin/vt
[14:51:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:08:58] This is snippy 4.6.0Show full stderr[15:08:58] This is snippy 4.6.0
[15:08:58] Written by Torsten Seemann
[15:08:58] Obtained from https://github.com/tseemann/snippy
[15:08:58] Detected operating system: linux
[15:08:58] Enabling bundled linux tools.
[15:08:58] Found bwa - /usr/local/bin/bwa
[15:08:58] Found bcftools - /usr/local/bin/bcftools
[15:08:58] Found samtools - /usr/local/bin/samtools
[15:08:58] Found java - /usr/local/bin/java
[15:08:58] Found snpEff - /usr/local/bin/snpEff
[15:08:58] Found samclip - /usr/local/bin/samclip
[15:08:58] Found seqtk - /usr/local/bin/seqtk
[15:08:58] Found parallel - /usr/local/bin/parallel
[15:08:58] Found freebayes - /usr/local/bin/freebayes
[15:08:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:08:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:08:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:08:58] Found vcfuniq - /usr/local/bin/vcfuniq
[15:08:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:08:58] Found gzip - /bin/gzip
[15:08:58] Found vt - /usr/local/bin/vt
[15:08:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:08:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:08:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:08:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:08:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:08:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:08:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:08:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:20] This is snippy 4.6.0Show full stderr[14:50:20] This is snippy 4.6.0
[14:50:20] Written by Torsten Seemann
[14:50:20] Obtained from https://github.com/tseemann/snippy
[14:50:20] Detected operating system: linux
[14:50:20] Enabling bundled linux tools.
[14:50:20] Found bwa - /usr/local/bin/bwa
[14:50:20] Found bcftools - /usr/local/bin/bcftools
[14:50:20] Found samtools - /usr/local/bin/samtools
[14:50:20] Found java - /usr/local/bin/java
[14:50:21] Found snpEff - /usr/local/bin/snpEff
[14:50:21] Found samclip - /usr/local/bin/samclip
[14:50:21] Found seqtk - /usr/local/bin/seqtk
[14:50:21] Found parallel - /usr/local/bin/parallel
[14:50:21] Found freebayes - /usr/local/bin/freebayes
[14:50:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:21] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:21] Found gzip - /bin/gzip
[14:50:21] Found vt - /usr/local/bin/vt
[14:50:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:15:52] This is snippy 4.6.0Show full stderr[15:15:52] This is snippy 4.6.0
[15:15:52] Written by Torsten Seemann
[15:15:52] Obtained from https://github.com/tseemann/snippy
[15:15:52] Detected operating system: linux
[15:15:52] Enabling bundled linux tools.
[15:15:52] Found bwa - /usr/local/bin/bwa
[15:15:52] Found bcftools - /usr/local/bin/bcftools
[15:15:52] Found samtools - /usr/local/bin/samtools
[15:15:52] Found java - /usr/local/bin/java
[15:15:52] Found snpEff - /usr/local/bin/snpEff
[15:15:52] Found samclip - /usr/local/bin/samclip
[15:15:52] Found seqtk - /usr/local/bin/seqtk
[15:15:52] Found parallel - /usr/local/bin/parallel
[15:15:52] Found freebayes - /usr/local/bin/freebayes
[15:15:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:15:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:15:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:15:52] Found vcfuniq - /usr/local/bin/vcfuniq
[15:15:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:15:52] Found gzip - /bin/gzip
[15:15:52] Found vt - /usr/local/bin/vt
[15:15:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:15:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:15:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:15:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:15:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:15:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:15:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:15:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:39] This is snippy 4.6.0Show full stderr[14:50:39] This is snippy 4.6.0
[14:50:39] Written by Torsten Seemann
[14:50:39] Obtained from https://github.com/tseemann/snippy
[14:50:39] Detected operating system: linux
[14:50:39] Enabling bundled linux tools.
[14:50:39] Found bwa - /usr/local/bin/bwa
[14:50:39] Found bcftools - /usr/local/bin/bcftools
[14:50:39] Found samtools - /usr/local/bin/samtools
[14:50:39] Found java - /usr/local/bin/java
[14:50:39] Found snpEff - /usr/local/bin/snpEff
[14:50:39] Found samclip - /usr/local/bin/samclip
[14:50:39] Found seqtk - /usr/local/bin/seqtk
[14:50:39] Found parallel - /usr/local/bin/parallel
[14:50:39] Found freebayes - /usr/local/bin/freebayes
[14:50:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:39] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:39] Found gzip - /bin/gzip
[14:50:39] Found vt - /usr/local/bin/vt
[14:50:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:40] This is snippy 4.6.0Show full stderr[14:50:40] This is snippy 4.6.0
[14:50:40] Written by Torsten Seemann
[14:50:40] Obtained from https://github.com/tseemann/snippy
[14:50:40] Detected operating system: linux
[14:50:40] Enabling bundled linux tools.
[14:50:40] Found bwa - /usr/local/bin/bwa
[14:50:40] Found bcftools - /usr/local/bin/bcftools
[14:50:40] Found samtools - /usr/local/bin/samtools
[14:50:40] Found java - /usr/local/bin/java
[14:50:40] Found snpEff - /usr/local/bin/snpEff
[14:50:40] Found samclip - /usr/local/bin/samclip
[14:50:40] Found seqtk - /usr/local/bin/seqtk
[14:50:40] Found parallel - /usr/local/bin/parallel
[14:50:40] Found freebayes - /usr/local/bin/freebayes
[14:50:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:40] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:40] Found gzip - /bin/gzip
[14:50:40] Found vt - /usr/local/bin/vt
[14:50:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:51:26] This is snippy 4.6.0Show full stderr[14:51:26] This is snippy 4.6.0
[14:51:26] Written by Torsten Seemann
[14:51:26] Obtained from https://github.com/tseemann/snippy
[14:51:26] Detected operating system: linux
[14:51:26] Enabling bundled linux tools.
[14:51:26] Found bwa - /usr/local/bin/bwa
[14:51:26] Found bcftools - /usr/local/bin/bcftools
[14:51:26] Found samtools - /usr/local/bin/samtools
[14:51:26] Found java - /usr/local/bin/java
[14:51:26] Found snpEff - /usr/local/bin/snpEff
[14:51:26] Found samclip - /usr/local/bin/samclip
[14:51:26] Found seqtk - /usr/local/bin/seqtk
[14:51:26] Found parallel - /usr/local/bin/parallel
[14:51:26] Found freebayes - /usr/local/bin/freebayes
[14:51:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:26] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:26] Found gzip - /bin/gzip
[14:51:26] Found vt - /usr/local/bin/vt
[14:51:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:52:09] This is snippy 4.6.0Show full stderr[14:52:09] This is snippy 4.6.0
[14:52:09] Written by Torsten Seemann
[14:52:09] Obtained from https://github.com/tseemann/snippy
[14:52:09] Detected operating system: linux
[14:52:09] Enabling bundled linux tools.
[14:52:09] Found bwa - /usr/local/bin/bwa
[14:52:09] Found bcftools - /usr/local/bin/bcftools
[14:52:09] Found samtools - /usr/local/bin/samtools
[14:52:09] Found java - /usr/local/bin/java
[14:52:09] Found snpEff - /usr/local/bin/snpEff
[14:52:09] Found samclip - /usr/local/bin/samclip
[14:52:09] Found seqtk - /usr/local/bin/seqtk
[14:52:09] Found parallel - /usr/local/bin/parallel
[14:52:09] Found freebayes - /usr/local/bin/freebayes
[14:52:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:52:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:52:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:52:09] Found vcfuniq - /usr/local/bin/vcfuniq
[14:52:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:52:09] Found gzip - /bin/gzip
[14:52:09] Found vt - /usr/local/bin/vt
[14:52:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:52:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:52:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:52:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:52:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:52:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:52:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:52:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:16:26] This is snippy 4.6.0Show full stderr[15:16:26] This is snippy 4.6.0
[15:16:26] Written by Torsten Seemann
[15:16:26] Obtained from https://github.com/tseemann/snippy
[15:16:26] Detected operating system: linux
[15:16:26] Enabling bundled linux tools.
[15:16:26] Found bwa - /usr/local/bin/bwa
[15:16:26] Found bcftools - /usr/local/bin/bcftools
[15:16:26] Found samtools - /usr/local/bin/samtools
[15:16:26] Found java - /usr/local/bin/java
[15:16:26] Found snpEff - /usr/local/bin/snpEff
[15:16:26] Found samclip - /usr/local/bin/samclip
[15:16:26] Found seqtk - /usr/local/bin/seqtk
[15:16:26] Found parallel - /usr/local/bin/parallel
[15:16:26] Found freebayes - /usr/local/bin/freebayes
[15:16:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:16:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:16:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:16:26] Found vcfuniq - /usr/local/bin/vcfuniq
[15:16:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:16:26] Found gzip - /bin/gzip
[15:16:26] Found vt - /usr/local/bin/vt
[15:16:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:16:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:16:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:16:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:16:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:16:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:16:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:16:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:52:24] This is snippy 4.6.0Show full stderr[14:52:24] This is snippy 4.6.0
[14:52:24] Written by Torsten Seemann
[14:52:24] Obtained from https://github.com/tseemann/snippy
[14:52:24] Detected operating system: linux
[14:52:24] Enabling bundled linux tools.
[14:52:24] Found bwa - /usr/local/bin/bwa
[14:52:24] Found bcftools - /usr/local/bin/bcftools
[14:52:24] Found samtools - /usr/local/bin/samtools
[14:52:24] Found java - /usr/local/bin/java
[14:52:24] Found snpEff - /usr/local/bin/snpEff
[14:52:24] Found samclip - /usr/local/bin/samclip
[14:52:24] Found seqtk - /usr/local/bin/seqtk
[14:52:24] Found parallel - /usr/local/bin/parallel
[14:52:24] Found freebayes - /usr/local/bin/freebayes
[14:52:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:52:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:52:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:52:24] Found vcfuniq - /usr/local/bin/vcfuniq
[14:52:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:52:24] Found gzip - /bin/gzip
[14:52:24] Found vt - /usr/local/bin/vt
[14:52:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:52:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:52:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:52:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:52:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:52:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:52:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:52:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:20:56] This is snippy 4.6.0Show full stderr[15:20:56] This is snippy 4.6.0
[15:20:56] Written by Torsten Seemann
[15:20:56] Obtained from https://github.com/tseemann/snippy
[15:20:56] Detected operating system: linux
[15:20:56] Enabling bundled linux tools.
[15:20:56] Found bwa - /usr/local/bin/bwa
[15:20:56] Found bcftools - /usr/local/bin/bcftools
[15:20:56] Found samtools - /usr/local/bin/samtools
[15:20:56] Found java - /usr/local/bin/java
[15:20:56] Found snpEff - /usr/local/bin/snpEff
[15:20:56] Found samclip - /usr/local/bin/samclip
[15:20:56] Found seqtk - /usr/local/bin/seqtk
[15:20:56] Found parallel - /usr/local/bin/parallel
[15:20:56] Found freebayes - /usr/local/bin/freebayes
[15:20:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:20:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:20:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:20:56] Found vcfuniq - /usr/local/bin/vcfuniq
[15:20:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:20:56] Found gzip - /bin/gzip
[15:20:56] Found vt - /usr/local/bin/vt
[15:20:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:20:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:20:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:20:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:20:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:20:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:20:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:20:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:22:26] This is snippy 4.6.0Show full stderr[15:22:26] This is snippy 4.6.0
[15:22:26] Written by Torsten Seemann
[15:22:26] Obtained from https://github.com/tseemann/snippy
[15:22:26] Detected operating system: linux
[15:22:26] Enabling bundled linux tools.
[15:22:26] Found bwa - /usr/local/bin/bwa
[15:22:26] Found bcftools - /usr/local/bin/bcftools
[15:22:26] Found samtools - /usr/local/bin/samtools
[15:22:26] Found java - /usr/local/bin/java
[15:22:26] Found snpEff - /usr/local/bin/snpEff
[15:22:26] Found samclip - /usr/local/bin/samclip
[15:22:26] Found seqtk - /usr/local/bin/seqtk
[15:22:26] Found parallel - /usr/local/bin/parallel
[15:22:26] Found freebayes - /usr/local/bin/freebayes
[15:22:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:22:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:22:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:22:26] Found vcfuniq - /usr/local/bin/vcfuniq
[15:22:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:22:26] Found gzip - /bin/gzip
[15:22:26] Found vt - /usr/local/bin/vt
[15:22:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:22:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:22:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:22:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:22:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:22:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:22:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:22:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:49:30] This is snippy 4.6.0Show full stderr[14:49:30] This is snippy 4.6.0
[14:49:30] Written by Torsten Seemann
[14:49:30] Obtained from https://github.com/tseemann/snippy
[14:49:30] Detected operating system: linux
[14:49:30] Enabling bundled linux tools.
[14:49:30] Found bwa - /usr/local/bin/bwa
[14:49:30] Found bcftools - /usr/local/bin/bcftools
[14:49:30] Found samtools - /usr/local/bin/samtools
[14:49:30] Found java - /usr/local/bin/java
[14:49:30] Found snpEff - /usr/local/bin/snpEff
[14:49:30] Found samclip - /usr/local/bin/samclip
[14:49:30] Found seqtk - /usr/local/bin/seqtk
[14:49:30] Found parallel - /usr/local/bin/parallel
[14:49:30] Found freebayes - /usr/local/bin/freebayes
[14:49:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:30] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:30] Found gzip - /bin/gzip
[14:49:30] Found vt - /usr/local/bin/vt
[14:49:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:49:52] This is snippy 4.6.0Show full stderr[14:49:52] This is snippy 4.6.0
[14:49:52] Written by Torsten Seemann
[14:49:52] Obtained from https://github.com/tseemann/snippy
[14:49:52] Detected operating system: linux
[14:49:52] Enabling bundled linux tools.
[14:49:52] Found bwa - /usr/local/bin/bwa
[14:49:52] Found bcftools - /usr/local/bin/bcftools
[14:49:52] Found samtools - /usr/local/bin/samtools
[14:49:52] Found java - /usr/local/bin/java
[14:49:52] Found snpEff - /usr/local/bin/snpEff
[14:49:52] Found samclip - /usr/local/bin/samclip
[14:49:52] Found seqtk - /usr/local/bin/seqtk
[14:49:52] Found parallel - /usr/local/bin/parallel
[14:49:52] Found freebayes - /usr/local/bin/freebayes
[14:49:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:52] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:52] Found gzip - /bin/gzip
[14:49:52] Found vt - /usr/local/bin/vt
[14:49:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:49:55] This is snippy 4.6.0Show full stderr[14:49:55] This is snippy 4.6.0
[14:49:55] Written by Torsten Seemann
[14:49:55] Obtained from https://github.com/tseemann/snippy
[14:49:55] Detected operating system: linux
[14:49:55] Enabling bundled linux tools.
[14:49:55] Found bwa - /usr/local/bin/bwa
[14:49:55] Found bcftools - /usr/local/bin/bcftools
[14:49:55] Found samtools - /usr/local/bin/samtools
[14:49:55] Found java - /usr/local/bin/java
[14:49:55] Found snpEff - /usr/local/bin/snpEff
[14:49:56] Found samclip - /usr/local/bin/samclip
[14:49:56] Found seqtk - /usr/local/bin/seqtk
[14:49:56] Found parallel - /usr/local/bin/parallel
[14:49:56] Found freebayes - /usr/local/bin/freebayes
[14:49:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:49:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:49:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:49:56] Found vcfuniq - /usr/local/bin/vcfuniq
[14:49:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:49:56] Found gzip - /bin/gzip
[14:49:56] Found vt - /usr/local/bin/vt
[14:49:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:49:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:49:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:49:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:49:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:49:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:49:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:49:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:24] This is snippy 4.6.0Show full stderr[14:50:24] This is snippy 4.6.0
[14:50:24] Written by Torsten Seemann
[14:50:24] Obtained from https://github.com/tseemann/snippy
[14:50:24] Detected operating system: linux
[14:50:24] Enabling bundled linux tools.
[14:50:24] Found bwa - /usr/local/bin/bwa
[14:50:24] Found bcftools - /usr/local/bin/bcftools
[14:50:24] Found samtools - /usr/local/bin/samtools
[14:50:24] Found java - /usr/local/bin/java
[14:50:24] Found snpEff - /usr/local/bin/snpEff
[14:50:24] Found samclip - /usr/local/bin/samclip
[14:50:24] Found seqtk - /usr/local/bin/seqtk
[14:50:24] Found parallel - /usr/local/bin/parallel
[14:50:24] Found freebayes - /usr/local/bin/freebayes
[14:50:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:24] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:24] Found gzip - /bin/gzip
[14:50:24] Found vt - /usr/local/bin/vt
[14:50:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:45] This is snippy 4.6.0Show full stderr[14:50:45] This is snippy 4.6.0
[14:50:45] Written by Torsten Seemann
[14:50:45] Obtained from https://github.com/tseemann/snippy
[14:50:45] Detected operating system: linux
[14:50:45] Enabling bundled linux tools.
[14:50:45] Found bwa - /usr/local/bin/bwa
[14:50:45] Found bcftools - /usr/local/bin/bcftools
[14:50:45] Found samtools - /usr/local/bin/samtools
[14:50:45] Found java - /usr/local/bin/java
[14:50:45] Found snpEff - /usr/local/bin/snpEff
[14:50:45] Found samclip - /usr/local/bin/samclip
[14:50:45] Found seqtk - /usr/local/bin/seqtk
[14:50:45] Found parallel - /usr/local/bin/parallel
[14:50:45] Found freebayes - /usr/local/bin/freebayes
[14:50:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:45] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:45] Found gzip - /bin/gzip
[14:50:45] Found vt - /usr/local/bin/vt
[14:50:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:51:39] This is snippy 4.6.0Show full stderr[14:51:39] This is snippy 4.6.0
[14:51:39] Written by Torsten Seemann
[14:51:39] Obtained from https://github.com/tseemann/snippy
[14:51:39] Detected operating system: linux
[14:51:39] Enabling bundled linux tools.
[14:51:39] Found bwa - /usr/local/bin/bwa
[14:51:40] Found bcftools - /usr/local/bin/bcftools
[14:51:40] Found samtools - /usr/local/bin/samtools
[14:51:40] Found java - /usr/local/bin/java
[14:51:40] Found snpEff - /usr/local/bin/snpEff
[14:51:40] Found samclip - /usr/local/bin/samclip
[14:51:40] Found seqtk - /usr/local/bin/seqtk
[14:51:40] Found parallel - /usr/local/bin/parallel
[14:51:40] Found freebayes - /usr/local/bin/freebayes
[14:51:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:40] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:40] Found gzip - /bin/gzip
[14:51:40] Found vt - /usr/local/bin/vt
[14:51:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:09:58] This is snippy 4.6.0Show full stderr[15:09:58] This is snippy 4.6.0
[15:09:58] Written by Torsten Seemann
[15:09:58] Obtained from https://github.com/tseemann/snippy
[15:09:58] Detected operating system: linux
[15:09:58] Enabling bundled linux tools.
[15:09:58] Found bwa - /usr/local/bin/bwa
[15:09:58] Found bcftools - /usr/local/bin/bcftools
[15:09:58] Found samtools - /usr/local/bin/samtools
[15:09:58] Found java - /usr/local/bin/java
[15:09:58] Found snpEff - /usr/local/bin/snpEff
[15:09:58] Found samclip - /usr/local/bin/samclip
[15:09:58] Found seqtk - /usr/local/bin/seqtk
[15:09:58] Found parallel - /usr/local/bin/parallel
[15:09:58] Found freebayes - /usr/local/bin/freebayes
[15:09:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:09:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:09:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:09:59] Found vcfuniq - /usr/local/bin/vcfuniq
[15:09:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:09:59] Found gzip - /bin/gzip
[15:09:59] Found vt - /usr/local/bin/vt
[15:09:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:09:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:09:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:09:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:09:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:09:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:09:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:09:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:10:25] This is snippy 4.6.0Show full stderr[15:10:25] This is snippy 4.6.0
[15:10:25] Written by Torsten Seemann
[15:10:25] Obtained from https://github.com/tseemann/snippy
[15:10:25] Detected operating system: linux
[15:10:25] Enabling bundled linux tools.
[15:10:25] Found bwa - /usr/local/bin/bwa
[15:10:25] Found bcftools - /usr/local/bin/bcftools
[15:10:25] Found samtools - /usr/local/bin/samtools
[15:10:25] Found java - /usr/local/bin/java
[15:10:25] Found snpEff - /usr/local/bin/snpEff
[15:10:25] Found samclip - /usr/local/bin/samclip
[15:10:25] Found seqtk - /usr/local/bin/seqtk
[15:10:25] Found parallel - /usr/local/bin/parallel
[15:10:25] Found freebayes - /usr/local/bin/freebayes
[15:10:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:10:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:10:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:10:25] Found vcfuniq - /usr/local/bin/vcfuniq
[15:10:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:10:25] Found gzip - /bin/gzip
[15:10:25] Found vt - /usr/local/bin/vt
[15:10:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:10:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:10:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:10:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:10:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:10:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:10:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:10:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:07] This is snippy 4.6.0Show full stderr[14:50:07] This is snippy 4.6.0
[14:50:07] Written by Torsten Seemann
[14:50:07] Obtained from https://github.com/tseemann/snippy
[14:50:07] Detected operating system: linux
[14:50:07] Enabling bundled linux tools.
[14:50:07] Found bwa - /usr/local/bin/bwa
[14:50:07] Found bcftools - /usr/local/bin/bcftools
[14:50:08] Found samtools - /usr/local/bin/samtools
[14:50:08] Found java - /usr/local/bin/java
[14:50:08] Found snpEff - /usr/local/bin/snpEff
[14:50:08] Found samclip - /usr/local/bin/samclip
[14:50:08] Found seqtk - /usr/local/bin/seqtk
[14:50:08] Found parallel - /usr/local/bin/parallel
[14:50:08] Found freebayes - /usr/local/bin/freebayes
[14:50:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:08] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:08] Found gzip - /bin/gzip
[14:50:08] Found vt - /usr/local/bin/vt
[14:50:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:09] This is snippy 4.6.0Show full stderr[14:50:09] This is snippy 4.6.0
[14:50:09] Written by Torsten Seemann
[14:50:09] Obtained from https://github.com/tseemann/snippy
[14:50:09] Detected operating system: linux
[14:50:09] Enabling bundled linux tools.
[14:50:09] Found bwa - /usr/local/bin/bwa
[14:50:09] Found bcftools - /usr/local/bin/bcftools
[14:50:09] Found samtools - /usr/local/bin/samtools
[14:50:09] Found java - /usr/local/bin/java
[14:50:09] Found snpEff - /usr/local/bin/snpEff
[14:50:09] Found samclip - /usr/local/bin/samclip
[14:50:09] Found seqtk - /usr/local/bin/seqtk
[14:50:09] Found parallel - /usr/local/bin/parallel
[14:50:09] Found freebayes - /usr/local/bin/freebayes
[14:50:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:09] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:09] Found gzip - /bin/gzip
[14:50:09] Found vt - /usr/local/bin/vt
[14:50:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:11] This is snippy 4.6.0Show full stderr[14:50:11] This is snippy 4.6.0
[14:50:11] Written by Torsten Seemann
[14:50:11] Obtained from https://github.com/tseemann/snippy
[14:50:11] Detected operating system: linux
[14:50:11] Enabling bundled linux tools.
[14:50:11] Found bwa - /usr/local/bin/bwa
[14:50:11] Found bcftools - /usr/local/bin/bcftools
[14:50:11] Found samtools - /usr/local/bin/samtools
[14:50:11] Found java - /usr/local/bin/java
[14:50:11] Found snpEff - /usr/local/bin/snpEff
[14:50:11] Found samclip - /usr/local/bin/samclip
[14:50:11] Found seqtk - /usr/local/bin/seqtk
[14:50:11] Found parallel - /usr/local/bin/parallel
[14:50:11] Found freebayes - /usr/local/bin/freebayes
[14:50:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:11] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:11] Found gzip - /bin/gzip
[14:50:11] Found vt - /usr/local/bin/vt
[14:50:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:15] This is snippy 4.6.0Show full stderr[14:50:15] This is snippy 4.6.0
[14:50:15] Written by Torsten Seemann
[14:50:15] Obtained from https://github.com/tseemann/snippy
[14:50:15] Detected operating system: linux
[14:50:15] Enabling bundled linux tools.
[14:50:15] Found bwa - /usr/local/bin/bwa
[14:50:15] Found bcftools - /usr/local/bin/bcftools
[14:50:15] Found samtools - /usr/local/bin/samtools
[14:50:15] Found java - /usr/local/bin/java
[14:50:15] Found snpEff - /usr/local/bin/snpEff
[14:50:15] Found samclip - /usr/local/bin/samclip
[14:50:15] Found seqtk - /usr/local/bin/seqtk
[14:50:15] Found parallel - /usr/local/bin/parallel
[14:50:15] Found freebayes - /usr/local/bin/freebayes
[14:50:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:15] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:15] Found gzip - /bin/gzip
[14:50:15] Found vt - /usr/local/bin/vt
[14:50:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:29] This is snippy 4.6.0Show full stderr[14:50:29] This is snippy 4.6.0
[14:50:29] Written by Torsten Seemann
[14:50:29] Obtained from https://github.com/tseemann/snippy
[14:50:29] Detected operating system: linux
[14:50:29] Enabling bundled linux tools.
[14:50:29] Found bwa - /usr/local/bin/bwa
[14:50:29] Found bcftools - /usr/local/bin/bcftools
[14:50:29] Found samtools - /usr/local/bin/samtools
[14:50:29] Found java - /usr/local/bin/java
[14:50:29] Found snpEff - /usr/local/bin/snpEff
[14:50:30] Found samclip - /usr/local/bin/samclip
[14:50:30] Found seqtk - /usr/local/bin/seqtk
[14:50:30] Found parallel - /usr/local/bin/parallel
[14:50:30] Found freebayes - /usr/local/bin/freebayes
[14:50:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:30] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:30] Found gzip - /bin/gzip
[14:50:30] Found vt - /usr/local/bin/vt
[14:50:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:36] This is snippy 4.6.0Show full stderr[14:50:36] This is snippy 4.6.0
[14:50:36] Written by Torsten Seemann
[14:50:36] Obtained from https://github.com/tseemann/snippy
[14:50:36] Detected operating system: linux
[14:50:36] Enabling bundled linux tools.
[14:50:36] Found bwa - /usr/local/bin/bwa
[14:50:36] Found bcftools - /usr/local/bin/bcftools
[14:50:36] Found samtools - /usr/local/bin/samtools
[14:50:36] Found java - /usr/local/bin/java
[14:50:36] Found snpEff - /usr/local/bin/snpEff
[14:50:36] Found samclip - /usr/local/bin/samclip
[14:50:36] Found seqtk - /usr/local/bin/seqtk
[14:50:36] Found parallel - /usr/local/bin/parallel
[14:50:36] Found freebayes - /usr/local/bin/freebayes
[14:50:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:36] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:36] Found gzip - /bin/gzip
[14:50:36] Found vt - /usr/local/bin/vt
[14:50:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:54] This is snippy 4.6.0Show full stderr[14:50:54] This is snippy 4.6.0
[14:50:54] Written by Torsten Seemann
[14:50:54] Obtained from https://github.com/tseemann/snippy
[14:50:54] Detected operating system: linux
[14:50:54] Enabling bundled linux tools.
[14:50:54] Found bwa - /usr/local/bin/bwa
[14:50:54] Found bcftools - /usr/local/bin/bcftools
[14:50:54] Found samtools - /usr/local/bin/samtools
[14:50:54] Found java - /usr/local/bin/java
[14:50:54] Found snpEff - /usr/local/bin/snpEff
[14:50:54] Found samclip - /usr/local/bin/samclip
[14:50:54] Found seqtk - /usr/local/bin/seqtk
[14:50:54] Found parallel - /usr/local/bin/parallel
[14:50:54] Found freebayes - /usr/local/bin/freebayes
[14:50:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:54] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:54] Found gzip - /bin/gzip
[14:50:54] Found vt - /usr/local/bin/vt
[14:50:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:50:56] This is snippy 4.6.0Show full stderr[14:50:56] This is snippy 4.6.0
[14:50:56] Written by Torsten Seemann
[14:50:56] Obtained from https://github.com/tseemann/snippy
[14:50:56] Detected operating system: linux
[14:50:56] Enabling bundled linux tools.
[14:50:56] Found bwa - /usr/local/bin/bwa
[14:50:56] Found bcftools - /usr/local/bin/bcftools
[14:50:56] Found samtools - /usr/local/bin/samtools
[14:50:56] Found java - /usr/local/bin/java
[14:50:56] Found snpEff - /usr/local/bin/snpEff
[14:50:56] Found samclip - /usr/local/bin/samclip
[14:50:56] Found seqtk - /usr/local/bin/seqtk
[14:50:56] Found parallel - /usr/local/bin/parallel
[14:50:56] Found freebayes - /usr/local/bin/freebayes
[14:50:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:50:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:50:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:50:57] Found vcfuniq - /usr/local/bin/vcfuniq
[14:50:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:50:57] Found gzip - /bin/gzip
[14:50:57] Found vt - /usr/local/bin/vt
[14:50:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:50:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:50:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:50:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:50:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:50:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:50:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:50:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:20:53] This is snippy 4.6.0Show full stderr[15:20:53] This is snippy 4.6.0
[15:20:53] Written by Torsten Seemann
[15:20:53] Obtained from https://github.com/tseemann/snippy
[15:20:53] Detected operating system: linux
[15:20:53] Enabling bundled linux tools.
[15:20:53] Found bwa - /usr/local/bin/bwa
[15:20:53] Found bcftools - /usr/local/bin/bcftools
[15:20:53] Found samtools - /usr/local/bin/samtools
[15:20:53] Found java - /usr/local/bin/java
[15:20:53] Found snpEff - /usr/local/bin/snpEff
[15:20:53] Found samclip - /usr/local/bin/samclip
[15:20:53] Found seqtk - /usr/local/bin/seqtk
[15:20:53] Found parallel - /usr/local/bin/parallel
[15:20:53] Found freebayes - /usr/local/bin/freebayes
[15:20:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:20:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:20:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:20:53] Found vcfuniq - /usr/local/bin/vcfuniq
[15:20:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:20:53] Found gzip - /bin/gzip
[15:20:53] Found vt - /usr/local/bin/vt
[15:20:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:20:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:20:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:20:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:20:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:20:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:20:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:20:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:52:05] This is snippy 4.6.0Show full stderr[14:52:05] This is snippy 4.6.0
[14:52:05] Written by Torsten Seemann
[14:52:05] Obtained from https://github.com/tseemann/snippy
[14:52:05] Detected operating system: linux
[14:52:05] Enabling bundled linux tools.
[14:52:05] Found bwa - /usr/local/bin/bwa
[14:52:05] Found bcftools - /usr/local/bin/bcftools
[14:52:05] Found samtools - /usr/local/bin/samtools
[14:52:05] Found java - /usr/local/bin/java
[14:52:05] Found snpEff - /usr/local/bin/snpEff
[14:52:05] Found samclip - /usr/local/bin/samclip
[14:52:05] Found seqtk - /usr/local/bin/seqtk
[14:52:05] Found parallel - /usr/local/bin/parallel
[14:52:05] Found freebayes - /usr/local/bin/freebayes
[14:52:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:52:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:52:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:52:05] Found vcfuniq - /usr/local/bin/vcfuniq
[14:52:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:52:05] Found gzip - /bin/gzip
[14:52:05] Found vt - /usr/local/bin/vt
[14:52:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:52:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:52:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:52:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:52:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:52:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:52:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:52:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:52:20] This is snippy 4.6.0Show full stderr[14:52:20] This is snippy 4.6.0
[14:52:20] Written by Torsten Seemann
[14:52:20] Obtained from https://github.com/tseemann/snippy
[14:52:20] Detected operating system: linux
[14:52:20] Enabling bundled linux tools.
[14:52:20] Found bwa - /usr/local/bin/bwa
[14:52:20] Found bcftools - /usr/local/bin/bcftools
[14:52:20] Found samtools - /usr/local/bin/samtools
[14:52:20] Found java - /usr/local/bin/java
[14:52:20] Found snpEff - /usr/local/bin/snpEff
[14:52:20] Found samclip - /usr/local/bin/samclip
[14:52:20] Found seqtk - /usr/local/bin/seqtk
[14:52:20] Found parallel - /usr/local/bin/parallel
[14:52:20] Found freebayes - /usr/local/bin/freebayes
[14:52:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:52:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:52:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:52:20] Found vcfuniq - /usr/local/bin/vcfuniq
[14:52:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:52:20] Found gzip - /bin/gzip
[14:52:20] Found vt - /usr/local/bin/vt
[14:52:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:52:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:52:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:52:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:52:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:52:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:52:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:52:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:52:50] This is snippy 4.6.0Show full stderr[14:52:50] This is snippy 4.6.0
[14:52:50] Written by Torsten Seemann
[14:52:50] Obtained from https://github.com/tseemann/snippy
[14:52:50] Detected operating system: linux
[14:52:50] Enabling bundled linux tools.
[14:52:50] Found bwa - /usr/local/bin/bwa
[14:52:50] Found bcftools - /usr/local/bin/bcftools
[14:52:50] Found samtools - /usr/local/bin/samtools
[14:52:50] Found java - /usr/local/bin/java
[14:52:50] Found snpEff - /usr/local/bin/snpEff
[14:52:50] Found samclip - /usr/local/bin/samclip
[14:52:50] Found seqtk - /usr/local/bin/seqtk
[14:52:50] Found parallel - /usr/local/bin/parallel
[14:52:50] Found freebayes - /usr/local/bin/freebayes
[14:52:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:52:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:52:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:52:50] Found vcfuniq - /usr/local/bin/vcfuniq
[14:52:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:52:50] Found gzip - /bin/gzip
[14:52:50] Found vt - /usr/local/bin/vt
[14:52:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:52:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:52:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:52:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:52:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:52:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:52:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:52:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:53:04] This is snippy 4.6.0Show full stderr[14:53:04] This is snippy 4.6.0
[14:53:04] Written by Torsten Seemann
[14:53:04] Obtained from https://github.com/tseemann/snippy
[14:53:04] Detected operating system: linux
[14:53:04] Enabling bundled linux tools.
[14:53:04] Found bwa - /usr/local/bin/bwa
[14:53:04] Found bcftools - /usr/local/bin/bcftools
[14:53:04] Found samtools - /usr/local/bin/samtools
[14:53:04] Found java - /usr/local/bin/java
[14:53:04] Found snpEff - /usr/local/bin/snpEff
[14:53:04] Found samclip - /usr/local/bin/samclip
[14:53:04] Found seqtk - /usr/local/bin/seqtk
[14:53:04] Found parallel - /usr/local/bin/parallel
[14:53:04] Found freebayes - /usr/local/bin/freebayes
[14:53:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:53:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:53:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:53:04] Found vcfuniq - /usr/local/bin/vcfuniq
[14:53:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:53:04] Found gzip - /bin/gzip
[14:53:04] Found vt - /usr/local/bin/vt
[14:53:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:53:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:53:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:53:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:53:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:53:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:53:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:53:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:53:09] This is snippy 4.6.0Show full stderr[14:53:09] This is snippy 4.6.0
[14:53:09] Written by Torsten Seemann
[14:53:09] Obtained from https://github.com/tseemann/snippy
[14:53:09] Detected operating system: linux
[14:53:09] Enabling bundled linux tools.
[14:53:09] Found bwa - /usr/local/bin/bwa
[14:53:09] Found bcftools - /usr/local/bin/bcftools
[14:53:09] Found samtools - /usr/local/bin/samtools
[14:53:09] Found java - /usr/local/bin/java
[14:53:09] Found snpEff - /usr/local/bin/snpEff
[14:53:09] Found samclip - /usr/local/bin/samclip
[14:53:09] Found seqtk - /usr/local/bin/seqtk
[14:53:09] Found parallel - /usr/local/bin/parallel
[14:53:09] Found freebayes - /usr/local/bin/freebayes
[14:53:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:53:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:53:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:53:09] Found vcfuniq - /usr/local/bin/vcfuniq
[14:53:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:53:09] Found gzip - /bin/gzip
[14:53:09] Found vt - /usr/local/bin/vt
[14:53:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:53:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:53:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:53:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:53:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:53:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:53:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:53:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:21:55] This is snippy 4.6.0Show full stderr[15:21:55] This is snippy 4.6.0
[15:21:55] Written by Torsten Seemann
[15:21:55] Obtained from https://github.com/tseemann/snippy
[15:21:55] Detected operating system: linux
[15:21:55] Enabling bundled linux tools.
[15:21:55] Found bwa - /usr/local/bin/bwa
[15:21:55] Found bcftools - /usr/local/bin/bcftools
[15:21:55] Found samtools - /usr/local/bin/samtools
[15:21:55] Found java - /usr/local/bin/java
[15:21:55] Found snpEff - /usr/local/bin/snpEff
[15:21:55] Found samclip - /usr/local/bin/samclip
[15:21:55] Found seqtk - /usr/local/bin/seqtk
[15:21:55] Found parallel - /usr/local/bin/parallel
[15:21:55] Found freebayes - /usr/local/bin/freebayes
[15:21:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:21:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:21:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:21:55] Found vcfuniq - /usr/local/bin/vcfuniq
[15:21:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:21:55] Found gzip - /bin/gzip
[15:21:55] Found vt - /usr/local/bin/vt
[15:21:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:21:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:21:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:21:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:21:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:21:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:21:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:21:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:26:55] This is snippy 4.6.0Show full stderr[15:26:55] This is snippy 4.6.0
[15:26:55] Written by Torsten Seemann
[15:26:55] Obtained from https://github.com/tseemann/snippy
[15:26:55] Detected operating system: linux
[15:26:55] Enabling bundled linux tools.
[15:26:55] Found bwa - /usr/local/bin/bwa
[15:26:55] Found bcftools - /usr/local/bin/bcftools
[15:26:55] Found samtools - /usr/local/bin/samtools
[15:26:55] Found java - /usr/local/bin/java
[15:26:55] Found snpEff - /usr/local/bin/snpEff
[15:26:55] Found samclip - /usr/local/bin/samclip
[15:26:55] Found seqtk - /usr/local/bin/seqtk
[15:26:55] Found parallel - /usr/local/bin/parallel
[15:26:55] Found freebayes - /usr/local/bin/freebayes
[15:26:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:26:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:26:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:26:55] Found vcfuniq - /usr/local/bin/vcfuniq
[15:26:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:26:55] Found gzip - /bin/gzip
[15:26:55] Found vt - /usr/local/bin/vt
[15:26:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:26:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:26:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:26:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:26:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:26:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:26:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:26:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:26:58] This is snippy 4.6.0Show full stderr[15:26:58] This is snippy 4.6.0
[15:26:58] Written by Torsten Seemann
[15:26:58] Obtained from https://github.com/tseemann/snippy
[15:26:58] Detected operating system: linux
[15:26:58] Enabling bundled linux tools.
[15:26:58] Found bwa - /usr/local/bin/bwa
[15:26:58] Found bcftools - /usr/local/bin/bcftools
[15:26:58] Found samtools - /usr/local/bin/samtools
[15:26:58] Found java - /usr/local/bin/java
[15:26:58] Found snpEff - /usr/local/bin/snpEff
[15:26:58] Found samclip - /usr/local/bin/samclip
[15:26:58] Found seqtk - /usr/local/bin/seqtk
[15:26:58] Found parallel - /usr/local/bin/parallel
[15:26:58] Found freebayes - /usr/local/bin/freebayes
[15:26:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:26:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:26:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:26:58] Found vcfuniq - /usr/local/bin/vcfuniq
[15:26:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:26:58] Found gzip - /bin/gzip
[15:26:58] Found vt - /usr/local/bin/vt
[15:26:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:26:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:26:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:26:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:26:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:26:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:26:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:26:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:27:54] This is snippy 4.6.0Show full stderr[15:27:54] This is snippy 4.6.0
[15:27:54] Written by Torsten Seemann
[15:27:54] Obtained from https://github.com/tseemann/snippy
[15:27:54] Detected operating system: linux
[15:27:54] Enabling bundled linux tools.
[15:27:54] Found bwa - /usr/local/bin/bwa
[15:27:54] Found bcftools - /usr/local/bin/bcftools
[15:27:54] Found samtools - /usr/local/bin/samtools
[15:27:54] Found java - /usr/local/bin/java
[15:27:54] Found snpEff - /usr/local/bin/snpEff
[15:27:54] Found samclip - /usr/local/bin/samclip
[15:27:54] Found seqtk - /usr/local/bin/seqtk
[15:27:54] Found parallel - /usr/local/bin/parallel
[15:27:54] Found freebayes - /usr/local/bin/freebayes
[15:27:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:27:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:27:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:27:54] Found vcfuniq - /usr/local/bin/vcfuniq
[15:27:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:27:54] Found gzip - /bin/gzip
[15:27:54] Found vt - /usr/local/bin/vt
[15:27:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:27:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:27:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:27:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:27:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:27:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:27:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:27:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:28:25] This is snippy 4.6.0Show full stderr[15:28:25] This is snippy 4.6.0
[15:28:25] Written by Torsten Seemann
[15:28:25] Obtained from https://github.com/tseemann/snippy
[15:28:25] Detected operating system: linux
[15:28:25] Enabling bundled linux tools.
[15:28:25] Found bwa - /usr/local/bin/bwa
[15:28:25] Found bcftools - /usr/local/bin/bcftools
[15:28:25] Found samtools - /usr/local/bin/samtools
[15:28:25] Found java - /usr/local/bin/java
[15:28:25] Found snpEff - /usr/local/bin/snpEff
[15:28:25] Found samclip - /usr/local/bin/samclip
[15:28:25] Found seqtk - /usr/local/bin/seqtk
[15:28:25] Found parallel - /usr/local/bin/parallel
[15:28:25] Found freebayes - /usr/local/bin/freebayes
[15:28:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:28:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:28:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:28:25] Found vcfuniq - /usr/local/bin/vcfuniq
[15:28:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:28:25] Found gzip - /bin/gzip
[15:28:25] Found vt - /usr/local/bin/vt
[15:28:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:28:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:28:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:28:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:28:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:28:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:28:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:28:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:32:57] This is snippy 4.6.0Show full stderr[15:32:57] This is snippy 4.6.0
[15:32:57] Written by Torsten Seemann
[15:32:57] Obtained from https://github.com/tseemann/snippy
[15:32:57] Detected operating system: linux
[15:32:57] Enabling bundled linux tools.
[15:32:57] Found bwa - /usr/local/bin/bwa
[15:32:57] Found bcftools - /usr/local/bin/bcftools
[15:32:57] Found samtools - /usr/local/bin/samtools
[15:32:57] Found java - /usr/local/bin/java
[15:32:57] Found snpEff - /usr/local/bin/snpEff
[15:32:57] Found samclip - /usr/local/bin/samclip
[15:32:57] Found seqtk - /usr/local/bin/seqtk
[15:32:57] Found parallel - /usr/local/bin/parallel
[15:32:57] Found freebayes - /usr/local/bin/freebayes
[15:32:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:32:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:32:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:32:57] Found vcfuniq - /usr/local/bin/vcfuniq
[15:32:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:32:57] Found gzip - /bin/gzip
[15:32:57] Found vt - /usr/local/bin/vt
[15:32:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:32:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:32:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:32:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:32:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:32:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:32:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:32:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:51:12] This is snippy 4.6.0Show full stderr[14:51:12] This is snippy 4.6.0
[14:51:12] Written by Torsten Seemann
[14:51:12] Obtained from https://github.com/tseemann/snippy
[14:51:12] Detected operating system: linux
[14:51:12] Enabling bundled linux tools.
[14:51:12] Found bwa - /usr/local/bin/bwa
[14:51:12] Found bcftools - /usr/local/bin/bcftools
[14:51:12] Found samtools - /usr/local/bin/samtools
[14:51:12] Found java - /usr/local/bin/java
[14:51:12] Found snpEff - /usr/local/bin/snpEff
[14:51:12] Found samclip - /usr/local/bin/samclip
[14:51:12] Found seqtk - /usr/local/bin/seqtk
[14:51:12] Found parallel - /usr/local/bin/parallel
[14:51:12] Found freebayes - /usr/local/bin/freebayes
[14:51:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:12] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:12] Found gzip - /bin/gzip
[14:51:12] Found vt - /usr/local/bin/vt
[14:51:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:51:14] This is snippy 4.6.0Show full stderr[14:51:14] This is snippy 4.6.0
[14:51:14] Written by Torsten Seemann
[14:51:14] Obtained from https://github.com/tseemann/snippy
[14:51:14] Detected operating system: linux
[14:51:14] Enabling bundled linux tools.
[14:51:14] Found bwa - /usr/local/bin/bwa
[14:51:14] Found bcftools - /usr/local/bin/bcftools
[14:51:14] Found samtools - /usr/local/bin/samtools
[14:51:14] Found java - /usr/local/bin/java
[14:51:14] Found snpEff - /usr/local/bin/snpEff
[14:51:14] Found samclip - /usr/local/bin/samclip
[14:51:14] Found seqtk - /usr/local/bin/seqtk
[14:51:14] Found parallel - /usr/local/bin/parallel
[14:51:14] Found freebayes - /usr/local/bin/freebayes
[14:51:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:15] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:15] Found gzip - /bin/gzip
[14:51:15] Found vt - /usr/local/bin/vt
[14:51:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:51:40] This is snippy 4.6.0Show full stderr[14:51:40] This is snippy 4.6.0
[14:51:40] Written by Torsten Seemann
[14:51:40] Obtained from https://github.com/tseemann/snippy
[14:51:40] Detected operating system: linux
[14:51:40] Enabling bundled linux tools.
[14:51:40] Found bwa - /usr/local/bin/bwa
[14:51:40] Found bcftools - /usr/local/bin/bcftools
[14:51:40] Found samtools - /usr/local/bin/samtools
[14:51:40] Found java - /usr/local/bin/java
[14:51:40] Found snpEff - /usr/local/bin/snpEff
[14:51:40] Found samclip - /usr/local/bin/samclip
[14:51:40] Found seqtk - /usr/local/bin/seqtk
[14:51:40] Found parallel - /usr/local/bin/parallel
[14:51:40] Found freebayes - /usr/local/bin/freebayes
[14:51:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:40] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:40] Found gzip - /bin/gzip
[14:51:40] Found vt - /usr/local/bin/vt
[14:51:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:51:51] This is snippy 4.6.0Show full stderr[14:51:51] This is snippy 4.6.0
[14:51:51] Written by Torsten Seemann
[14:51:51] Obtained from https://github.com/tseemann/snippy
[14:51:51] Detected operating system: linux
[14:51:51] Enabling bundled linux tools.
[14:51:51] Found bwa - /usr/local/bin/bwa
[14:51:51] Found bcftools - /usr/local/bin/bcftools
[14:51:51] Found samtools - /usr/local/bin/samtools
[14:51:51] Found java - /usr/local/bin/java
[14:51:51] Found snpEff - /usr/local/bin/snpEff
[14:51:51] Found samclip - /usr/local/bin/samclip
[14:51:51] Found seqtk - /usr/local/bin/seqtk
[14:51:51] Found parallel - /usr/local/bin/parallel
[14:51:51] Found freebayes - /usr/local/bin/freebayes
[14:51:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:51:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:51:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:51:51] Found vcfuniq - /usr/local/bin/vcfuniq
[14:51:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:51:51] Found gzip - /bin/gzip
[14:51:51] Found vt - /usr/local/bin/vt
[14:51:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:51:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:51:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:51:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:51:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:51:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:51:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:51:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:15:56] This is snippy 4.6.0Show full stderr[15:15:56] This is snippy 4.6.0
[15:15:56] Written by Torsten Seemann
[15:15:56] Obtained from https://github.com/tseemann/snippy
[15:15:56] Detected operating system: linux
[15:15:56] Enabling bundled linux tools.
[15:15:56] Found bwa - /usr/local/bin/bwa
[15:15:56] Found bcftools - /usr/local/bin/bcftools
[15:15:56] Found samtools - /usr/local/bin/samtools
[15:15:56] Found java - /usr/local/bin/java
[15:15:56] Found snpEff - /usr/local/bin/snpEff
[15:15:56] Found samclip - /usr/local/bin/samclip
[15:15:56] Found seqtk - /usr/local/bin/seqtk
[15:15:56] Found parallel - /usr/local/bin/parallel
[15:15:56] Found freebayes - /usr/local/bin/freebayes
[15:15:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:15:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:15:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:15:56] Found vcfuniq - /usr/local/bin/vcfuniq
[15:15:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:15:56] Found gzip - /bin/gzip
[15:15:56] Found vt - /usr/local/bin/vt
[15:15:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:15:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:15:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:15:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:15:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:15:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:15:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:15:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:32:26] This is snippy 4.6.0Show full stderr[15:32:26] This is snippy 4.6.0
[15:32:26] Written by Torsten Seemann
[15:32:26] Obtained from https://github.com/tseemann/snippy
[15:32:26] Detected operating system: linux
[15:32:26] Enabling bundled linux tools.
[15:32:26] Found bwa - /usr/local/bin/bwa
[15:32:26] Found bcftools - /usr/local/bin/bcftools
[15:32:26] Found samtools - /usr/local/bin/samtools
[15:32:26] Found java - /usr/local/bin/java
[15:32:26] Found snpEff - /usr/local/bin/snpEff
[15:32:26] Found samclip - /usr/local/bin/samclip
[15:32:26] Found seqtk - /usr/local/bin/seqtk
[15:32:26] Found parallel - /usr/local/bin/parallel
[15:32:26] Found freebayes - /usr/local/bin/freebayes
[15:32:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:32:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:32:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:32:26] Found vcfuniq - /usr/local/bin/vcfuniq
[15:32:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:32:26] Found gzip - /bin/gzip
[15:32:26] Found vt - /usr/local/bin/vt
[15:32:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:32:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:32:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:32:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:32:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:32:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:32:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:32:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:40:30] This is snippy 4.6.0Show full stderr[15:40:30] This is snippy 4.6.0
[15:40:30] Written by Torsten Seemann
[15:40:30] Obtained from https://github.com/tseemann/snippy
[15:40:30] Detected operating system: linux
[15:40:30] Enabling bundled linux tools.
[15:40:30] Found bwa - /usr/local/bin/bwa
[15:40:30] Found bcftools - /usr/local/bin/bcftools
[15:40:30] Found samtools - /usr/local/bin/samtools
[15:40:30] Found java - /usr/local/bin/java
[15:40:30] Found snpEff - /usr/local/bin/snpEff
[15:40:30] Found samclip - /usr/local/bin/samclip
[15:40:30] Found seqtk - /usr/local/bin/seqtk
[15:40:30] Found parallel - /usr/local/bin/parallel
[15:40:30] Found freebayes - /usr/local/bin/freebayes
[15:40:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:40:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:40:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:40:30] Found vcfuniq - /usr/local/bin/vcfuniq
[15:40:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:40:30] Found gzip - /bin/gzip
[15:40:30] Found vt - /usr/local/bin/vt
[15:40:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:40:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:40:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:40:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:40:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:40:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:40:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:40:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:56:12] This is snippy 4.6.0Show full stderr[15:56:12] This is snippy 4.6.0
[15:56:12] Written by Torsten Seemann
[15:56:12] Obtained from https://github.com/tseemann/snippy
[15:56:12] Detected operating system: linux
[15:56:12] Enabling bundled linux tools.
[15:56:12] Found bwa - /usr/local/bin/bwa
[15:56:12] Found bcftools - /usr/local/bin/bcftools
[15:56:12] Found samtools - /usr/local/bin/samtools
[15:56:12] Found java - /usr/local/bin/java
[15:56:12] Found snpEff - /usr/local/bin/snpEff
[15:56:12] Found samclip - /usr/local/bin/samclip
[15:56:12] Found seqtk - /usr/local/bin/seqtk
[15:56:12] Found parallel - /usr/local/bin/parallel
[15:56:12] Found freebayes - /usr/local/bin/freebayes
[15:56:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:56:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:56:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:56:12] Found vcfuniq - /usr/local/bin/vcfuniq
[15:56:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:56:12] Found gzip - /bin/gzip
[15:56:12] Found vt - /usr/local/bin/vt
[15:56:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:56:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:56:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:56:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:56:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:56:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:56:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:56:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [16:04:27] This is snippy 4.6.0Show full stderr[16:04:27] This is snippy 4.6.0
[16:04:27] Written by Torsten Seemann
[16:04:27] Obtained from https://github.com/tseemann/snippy
[16:04:27] Detected operating system: linux
[16:04:27] Enabling bundled linux tools.
[16:04:27] Found bwa - /usr/local/bin/bwa
[16:04:27] Found bcftools - /usr/local/bin/bcftools
[16:04:27] Found samtools - /usr/local/bin/samtools
[16:04:27] Found java - /usr/local/bin/java
[16:04:27] Found snpEff - /usr/local/bin/snpEff
[16:04:27] Found samclip - /usr/local/bin/samclip
[16:04:27] Found seqtk - /usr/local/bin/seqtk
[16:04:27] Found parallel - /usr/local/bin/parallel
[16:04:27] Found freebayes - /usr/local/bin/freebayes
[16:04:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:04:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:04:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:04:27] Found vcfuniq - /usr/local/bin/vcfuniq
[16:04:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:04:27] Found gzip - /bin/gzip
[16:04:27] Found vt - /usr/local/bin/vt
[16:04:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:04:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:04:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:04:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:04:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:04:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:04:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:04:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [16:36:08] This is snippy 4.6.0Show full stderr[16:36:08] This is snippy 4.6.0
[16:36:08] Written by Torsten Seemann
[16:36:08] Obtained from https://github.com/tseemann/snippy
[16:36:08] Detected operating system: linux
[16:36:08] Enabling bundled linux tools.
[16:36:08] Found bwa - /usr/local/bin/bwa
[16:36:08] Found bcftools - /usr/local/bin/bcftools
[16:36:08] Found samtools - /usr/local/bin/samtools
[16:36:08] Found java - /usr/local/bin/java
[16:36:08] Found snpEff - /usr/local/bin/snpEff
[16:36:08] Found samclip - /usr/local/bin/samclip
[16:36:08] Found seqtk - /usr/local/bin/seqtk
[16:36:08] Found parallel - /usr/local/bin/parallel
[16:36:08] Found freebayes - /usr/local/bin/freebayes
[16:36:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:36:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:36:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:36:08] Found vcfuniq - /usr/local/bin/vcfuniq
[16:36:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:36:08] Found gzip - /bin/gzip
[16:36:08] Found vt - /usr/local/bin/vt
[16:36:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:36:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:36:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:36:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:36:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:36:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:36:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:36:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [16:43:56] This is snippy 4.6.0Show full stderr[16:43:56] This is snippy 4.6.0
[16:43:56] Written by Torsten Seemann
[16:43:56] Obtained from https://github.com/tseemann/snippy
[16:43:56] Detected operating system: linux
[16:43:56] Enabling bundled linux tools.
[16:43:56] Found bwa - /usr/local/bin/bwa
[16:43:56] Found bcftools - /usr/local/bin/bcftools
[16:43:56] Found samtools - /usr/local/bin/samtools
[16:43:56] Found java - /usr/local/bin/java
[16:43:56] Found snpEff - /usr/local/bin/snpEff
[16:43:56] Found samclip - /usr/local/bin/samclip
[16:43:56] Found seqtk - /usr/local/bin/seqtk
[16:43:56] Found parallel - /usr/local/bin/parallel
[16:43:56] Found freebayes - /usr/local/bin/freebayes
[16:43:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:43:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:43:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:43:56] Found vcfuniq - /usr/local/bin/vcfuniq
[16:43:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:43:56] Found gzip - /bin/gzip
[16:43:56] Found vt - /usr/local/bin/vt
[16:43:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:43:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:43:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:43:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:43:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:43:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:43:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:43:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [16:52:12] This is snippy 4.6.0Show full stderr[16:52:12] This is snippy 4.6.0
[16:52:12] Written by Torsten Seemann
[16:52:12] Obtained from https://github.com/tseemann/snippy
[16:52:12] Detected operating system: linux
[16:52:12] Enabling bundled linux tools.
[16:52:12] Found bwa - /usr/local/bin/bwa
[16:52:12] Found bcftools - /usr/local/bin/bcftools
[16:52:12] Found samtools - /usr/local/bin/samtools
[16:52:12] Found java - /usr/local/bin/java
[16:52:12] Found snpEff - /usr/local/bin/snpEff
[16:52:12] Found samclip - /usr/local/bin/samclip
[16:52:12] Found seqtk - /usr/local/bin/seqtk
[16:52:12] Found parallel - /usr/local/bin/parallel
[16:52:12] Found freebayes - /usr/local/bin/freebayes
[16:52:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:52:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:52:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:52:12] Found vcfuniq - /usr/local/bin/vcfuniq
[16:52:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:52:12] Found gzip - /bin/gzip
[16:52:12] Found vt - /usr/local/bin/vt
[16:52:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:52:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:52:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:52:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:52:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:52:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:52:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:52:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:00:10] This is snippy 4.6.0Show full stderr[17:00:10] This is snippy 4.6.0
[17:00:10] Written by Torsten Seemann
[17:00:10] Obtained from https://github.com/tseemann/snippy
[17:00:10] Detected operating system: linux
[17:00:10] Enabling bundled linux tools.
[17:00:10] Found bwa - /usr/local/bin/bwa
[17:00:10] Found bcftools - /usr/local/bin/bcftools
[17:00:10] Found samtools - /usr/local/bin/samtools
[17:00:10] Found java - /usr/local/bin/java
[17:00:10] Found snpEff - /usr/local/bin/snpEff
[17:00:10] Found samclip - /usr/local/bin/samclip
[17:00:10] Found seqtk - /usr/local/bin/seqtk
[17:00:10] Found parallel - /usr/local/bin/parallel
[17:00:10] Found freebayes - /usr/local/bin/freebayes
[17:00:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:00:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:00:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:00:10] Found vcfuniq - /usr/local/bin/vcfuniq
[17:00:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:00:10] Found gzip - /bin/gzip
[17:00:10] Found vt - /usr/local/bin/vt
[17:00:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:00:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:00:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:00:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:00:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:00:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:00:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:00:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:07:59] This is snippy 4.6.0Show full stderr[17:07:59] This is snippy 4.6.0
[17:07:59] Written by Torsten Seemann
[17:07:59] Obtained from https://github.com/tseemann/snippy
[17:07:59] Detected operating system: linux
[17:07:59] Enabling bundled linux tools.
[17:07:59] Found bwa - /usr/local/bin/bwa
[17:07:59] Found bcftools - /usr/local/bin/bcftools
[17:07:59] Found samtools - /usr/local/bin/samtools
[17:07:59] Found java - /usr/local/bin/java
[17:07:59] Found snpEff - /usr/local/bin/snpEff
[17:07:59] Found samclip - /usr/local/bin/samclip
[17:07:59] Found seqtk - /usr/local/bin/seqtk
[17:07:59] Found parallel - /usr/local/bin/parallel
[17:07:59] Found freebayes - /usr/local/bin/freebayes
[17:07:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:07:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:07:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:07:59] Found vcfuniq - /usr/local/bin/vcfuniq
[17:07:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:07:59] Found gzip - /bin/gzip
[17:07:59] Found vt - /usr/local/bin/vt
[17:07:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:07:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:07:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:07:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:07:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:08:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:08:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:08:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:09:15] This is snippy 4.6.0Show full stderr[17:09:15] This is snippy 4.6.0
[17:09:15] Written by Torsten Seemann
[17:09:15] Obtained from https://github.com/tseemann/snippy
[17:09:15] Detected operating system: linux
[17:09:15] Enabling bundled linux tools.
[17:09:15] Found bwa - /usr/local/bin/bwa
[17:09:15] Found bcftools - /usr/local/bin/bcftools
[17:09:15] Found samtools - /usr/local/bin/samtools
[17:09:15] Found java - /usr/local/bin/java
[17:09:15] Found snpEff - /usr/local/bin/snpEff
[17:09:15] Found samclip - /usr/local/bin/samclip
[17:09:15] Found seqtk - /usr/local/bin/seqtk
[17:09:15] Found parallel - /usr/local/bin/parallel
[17:09:15] Found freebayes - /usr/local/bin/freebayes
[17:09:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:09:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:09:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:09:15] Found vcfuniq - /usr/local/bin/vcfuniq
[17:09:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:09:15] Found gzip - /bin/gzip
[17:09:15] Found vt - /usr/local/bin/vt
[17:09:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:09:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:09:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:09:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:09:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:09:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:09:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:09:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:53:17] This is snippy 4.6.0Show full stderr[17:53:17] This is snippy 4.6.0
[17:53:17] Written by Torsten Seemann
[17:53:17] Obtained from https://github.com/tseemann/snippy
[17:53:17] Detected operating system: linux
[17:53:17] Enabling bundled linux tools.
[17:53:17] Found bwa - /usr/local/bin/bwa
[17:53:17] Found bcftools - /usr/local/bin/bcftools
[17:53:17] Found samtools - /usr/local/bin/samtools
[17:53:17] Found java - /usr/local/bin/java
[17:53:17] Found snpEff - /usr/local/bin/snpEff
[17:53:17] Found samclip - /usr/local/bin/samclip
[17:53:17] Found seqtk - /usr/local/bin/seqtk
[17:53:17] Found parallel - /usr/local/bin/parallel
[17:53:17] Found freebayes - /usr/local/bin/freebayes
[17:53:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:53:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:53:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:53:17] Found vcfuniq - /usr/local/bin/vcfuniq
[17:53:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:53:17] Found gzip - /bin/gzip
[17:53:17] Found vt - /usr/local/bin/vt
[17:53:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:53:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:53:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:53:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:53:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:53:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:53:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:53:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:01:18] This is snippy 4.6.0Show full stderr[18:01:18] This is snippy 4.6.0
[18:01:18] Written by Torsten Seemann
[18:01:18] Obtained from https://github.com/tseemann/snippy
[18:01:18] Detected operating system: linux
[18:01:18] Enabling bundled linux tools.
[18:01:18] Found bwa - /usr/local/bin/bwa
[18:01:18] Found bcftools - /usr/local/bin/bcftools
[18:01:18] Found samtools - /usr/local/bin/samtools
[18:01:18] Found java - /usr/local/bin/java
[18:01:18] Found snpEff - /usr/local/bin/snpEff
[18:01:18] Found samclip - /usr/local/bin/samclip
[18:01:18] Found seqtk - /usr/local/bin/seqtk
[18:01:18] Found parallel - /usr/local/bin/parallel
[18:01:18] Found freebayes - /usr/local/bin/freebayes
[18:01:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:01:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:01:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:01:18] Found vcfuniq - /usr/local/bin/vcfuniq
[18:01:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:01:18] Found gzip - /bin/gzip
[18:01:18] Found vt - /usr/local/bin/vt
[18:01:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:01:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:01:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:01:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:01:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:01:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:01:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:01:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:09:12] This is snippy 4.6.0Show full stderr[18:09:12] This is snippy 4.6.0
[18:09:12] Written by Torsten Seemann
[18:09:12] Obtained from https://github.com/tseemann/snippy
[18:09:12] Detected operating system: linux
[18:09:12] Enabling bundled linux tools.
[18:09:12] Found bwa - /usr/local/bin/bwa
[18:09:12] Found bcftools - /usr/local/bin/bcftools
[18:09:12] Found samtools - /usr/local/bin/samtools
[18:09:12] Found java - /usr/local/bin/java
[18:09:12] Found snpEff - /usr/local/bin/snpEff
[18:09:12] Found samclip - /usr/local/bin/samclip
[18:09:12] Found seqtk - /usr/local/bin/seqtk
[18:09:12] Found parallel - /usr/local/bin/parallel
[18:09:12] Found freebayes - /usr/local/bin/freebayes
[18:09:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:09:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:09:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:09:13] Found vcfuniq - /usr/local/bin/vcfuniq
[18:09:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:09:13] Found gzip - /bin/gzip
[18:09:13] Found vt - /usr/local/bin/vt
[18:09:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:09:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:09:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:09:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:09:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:09:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:09:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:09:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:17:57] This is snippy 4.6.0Show full stderr[18:17:57] This is snippy 4.6.0
[18:17:57] Written by Torsten Seemann
[18:17:57] Obtained from https://github.com/tseemann/snippy
[18:17:57] Detected operating system: linux
[18:17:57] Enabling bundled linux tools.
[18:17:57] Found bwa - /usr/local/bin/bwa
[18:17:57] Found bcftools - /usr/local/bin/bcftools
[18:17:57] Found samtools - /usr/local/bin/samtools
[18:17:57] Found java - /usr/local/bin/java
[18:17:57] Found snpEff - /usr/local/bin/snpEff
[18:17:57] Found samclip - /usr/local/bin/samclip
[18:17:57] Found seqtk - /usr/local/bin/seqtk
[18:17:57] Found parallel - /usr/local/bin/parallel
[18:17:57] Found freebayes - /usr/local/bin/freebayes
[18:17:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:17:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:17:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:17:57] Found vcfuniq - /usr/local/bin/vcfuniq
[18:17:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:17:57] Found gzip - /bin/gzip
[18:17:57] Found vt - /usr/local/bin/vt
[18:17:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:17:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:17:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:17:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:17:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:17:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:17:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:17:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:40:12] This is snippy 4.6.0Show full stderr[15:40:12] This is snippy 4.6.0
[15:40:12] Written by Torsten Seemann
[15:40:12] Obtained from https://github.com/tseemann/snippy
[15:40:12] Detected operating system: linux
[15:40:12] Enabling bundled linux tools.
[15:40:12] Found bwa - /usr/local/bin/bwa
[15:40:12] Found bcftools - /usr/local/bin/bcftools
[15:40:12] Found samtools - /usr/local/bin/samtools
[15:40:12] Found java - /usr/local/bin/java
[15:40:12] Found snpEff - /usr/local/bin/snpEff
[15:40:12] Found samclip - /usr/local/bin/samclip
[15:40:12] Found seqtk - /usr/local/bin/seqtk
[15:40:12] Found parallel - /usr/local/bin/parallel
[15:40:12] Found freebayes - /usr/local/bin/freebayes
[15:40:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:40:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:40:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:40:12] Found vcfuniq - /usr/local/bin/vcfuniq
[15:40:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:40:12] Found gzip - /bin/gzip
[15:40:12] Found vt - /usr/local/bin/vt
[15:40:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:40:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:40:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:40:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:40:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:40:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:40:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:40:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:56:46] This is snippy 4.6.0Show full stderr[15:56:46] This is snippy 4.6.0
[15:56:46] Written by Torsten Seemann
[15:56:46] Obtained from https://github.com/tseemann/snippy
[15:56:46] Detected operating system: linux
[15:56:46] Enabling bundled linux tools.
[15:56:46] Found bwa - /usr/local/bin/bwa
[15:56:46] Found bcftools - /usr/local/bin/bcftools
[15:56:46] Found samtools - /usr/local/bin/samtools
[15:56:46] Found java - /usr/local/bin/java
[15:56:46] Found snpEff - /usr/local/bin/snpEff
[15:56:46] Found samclip - /usr/local/bin/samclip
[15:56:46] Found seqtk - /usr/local/bin/seqtk
[15:56:46] Found parallel - /usr/local/bin/parallel
[15:56:46] Found freebayes - /usr/local/bin/freebayes
[15:56:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:56:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:56:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:56:46] Found vcfuniq - /usr/local/bin/vcfuniq
[15:56:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:56:46] Found gzip - /bin/gzip
[15:56:46] Found vt - /usr/local/bin/vt
[15:56:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:56:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:56:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:56:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:56:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:56:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:56:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:56:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [16:28:18] This is snippy 4.6.0Show full stderr[16:28:18] This is snippy 4.6.0
[16:28:18] Written by Torsten Seemann
[16:28:18] Obtained from https://github.com/tseemann/snippy
[16:28:18] Detected operating system: linux
[16:28:18] Enabling bundled linux tools.
[16:28:18] Found bwa - /usr/local/bin/bwa
[16:28:18] Found bcftools - /usr/local/bin/bcftools
[16:28:18] Found samtools - /usr/local/bin/samtools
[16:28:18] Found java - /usr/local/bin/java
[16:28:18] Found snpEff - /usr/local/bin/snpEff
[16:28:18] Found samclip - /usr/local/bin/samclip
[16:28:18] Found seqtk - /usr/local/bin/seqtk
[16:28:18] Found parallel - /usr/local/bin/parallel
[16:28:18] Found freebayes - /usr/local/bin/freebayes
[16:28:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:28:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:28:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:28:18] Found vcfuniq - /usr/local/bin/vcfuniq
[16:28:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:28:18] Found gzip - /bin/gzip
[16:28:18] Found vt - /usr/local/bin/vt
[16:28:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:28:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:28:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:28:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:28:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:28:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:28:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:28:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:47] This is snippy 4.6.0Show full stderr[17:26:47] This is snippy 4.6.0
[17:26:47] Written by Torsten Seemann
[17:26:47] Obtained from https://github.com/tseemann/snippy
[17:26:47] Detected operating system: linux
[17:26:47] Enabling bundled linux tools.
[17:26:47] Found bwa - /usr/local/bin/bwa
[17:26:47] Found bcftools - /usr/local/bin/bcftools
[17:26:47] Found samtools - /usr/local/bin/samtools
[17:26:47] Found java - /usr/local/bin/java
[17:26:47] Found snpEff - /usr/local/bin/snpEff
[17:26:47] Found samclip - /usr/local/bin/samclip
[17:26:47] Found seqtk - /usr/local/bin/seqtk
[17:26:47] Found parallel - /usr/local/bin/parallel
[17:26:47] Found freebayes - /usr/local/bin/freebayes
[17:26:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:47] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:47] Found gzip - /bin/gzip
[17:26:47] Found vt - /usr/local/bin/vt
[17:26:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:34:48] This is snippy 4.6.0Show full stderr[17:34:48] This is snippy 4.6.0
[17:34:48] Written by Torsten Seemann
[17:34:48] Obtained from https://github.com/tseemann/snippy
[17:34:48] Detected operating system: linux
[17:34:48] Enabling bundled linux tools.
[17:34:48] Found bwa - /usr/local/bin/bwa
[17:34:48] Found bcftools - /usr/local/bin/bcftools
[17:34:48] Found samtools - /usr/local/bin/samtools
[17:34:48] Found java - /usr/local/bin/java
[17:34:48] Found snpEff - /usr/local/bin/snpEff
[17:34:48] Found samclip - /usr/local/bin/samclip
[17:34:48] Found seqtk - /usr/local/bin/seqtk
[17:34:48] Found parallel - /usr/local/bin/parallel
[17:34:48] Found freebayes - /usr/local/bin/freebayes
[17:34:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:34:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:34:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:34:48] Found vcfuniq - /usr/local/bin/vcfuniq
[17:34:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:34:48] Found gzip - /bin/gzip
[17:34:48] Found vt - /usr/local/bin/vt
[17:34:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:34:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:34:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:34:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:34:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:34:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:34:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:34:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:20:53] This is snippy 4.6.0Show full stderr[21:20:53] This is snippy 4.6.0
[21:20:53] Written by Torsten Seemann
[21:20:53] Obtained from https://github.com/tseemann/snippy
[21:20:53] Detected operating system: linux
[21:20:53] Enabling bundled linux tools.
[21:20:53] Found bwa - /usr/local/bin/bwa
[21:20:53] Found bcftools - /usr/local/bin/bcftools
[21:20:53] Found samtools - /usr/local/bin/samtools
[21:20:53] Found java - /usr/local/bin/java
[21:20:53] Found snpEff - /usr/local/bin/snpEff
[21:20:53] Found samclip - /usr/local/bin/samclip
[21:20:53] Found seqtk - /usr/local/bin/seqtk
[21:20:53] Found parallel - /usr/local/bin/parallel
[21:20:53] Found freebayes - /usr/local/bin/freebayes
[21:20:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:20:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:20:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:20:53] Found vcfuniq - /usr/local/bin/vcfuniq
[21:20:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:20:53] Found gzip - /bin/gzip
[21:20:53] Found vt - /usr/local/bin/vt
[21:20:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:20:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:20:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:20:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:20:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:20:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:20:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:20:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:03:34] This is snippy 4.6.0Show full stderr[22:03:34] This is snippy 4.6.0
[22:03:34] Written by Torsten Seemann
[22:03:34] Obtained from https://github.com/tseemann/snippy
[22:03:34] Detected operating system: linux
[22:03:34] Enabling bundled linux tools.
[22:03:34] Found bwa - /usr/local/bin/bwa
[22:03:34] Found bcftools - /usr/local/bin/bcftools
[22:03:34] Found samtools - /usr/local/bin/samtools
[22:03:34] Found java - /usr/local/bin/java
[22:03:34] Found snpEff - /usr/local/bin/snpEff
[22:03:34] Found samclip - /usr/local/bin/samclip
[22:03:34] Found seqtk - /usr/local/bin/seqtk
[22:03:34] Found parallel - /usr/local/bin/parallel
[22:03:34] Found freebayes - /usr/local/bin/freebayes
[22:03:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:03:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:03:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:03:34] Found vcfuniq - /usr/local/bin/vcfuniq
[22:03:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:03:34] Found gzip - /bin/gzip
[22:03:34] Found vt - /usr/local/bin/vt
[22:03:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:03:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:03:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:03:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:03:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:03:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:03:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:03:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:45:17] This is snippy 4.6.0Show full stderr[22:45:17] This is snippy 4.6.0
[22:45:17] Written by Torsten Seemann
[22:45:17] Obtained from https://github.com/tseemann/snippy
[22:45:17] Detected operating system: linux
[22:45:17] Enabling bundled linux tools.
[22:45:17] Found bwa - /usr/local/bin/bwa
[22:45:17] Found bcftools - /usr/local/bin/bcftools
[22:45:17] Found samtools - /usr/local/bin/samtools
[22:45:17] Found java - /usr/local/bin/java
[22:45:17] Found snpEff - /usr/local/bin/snpEff
[22:45:17] Found samclip - /usr/local/bin/samclip
[22:45:17] Found seqtk - /usr/local/bin/seqtk
[22:45:17] Found parallel - /usr/local/bin/parallel
[22:45:17] Found freebayes - /usr/local/bin/freebayes
[22:45:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:45:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:45:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:45:17] Found vcfuniq - /usr/local/bin/vcfuniq
[22:45:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:45:17] Found gzip - /bin/gzip
[22:45:17] Found vt - /usr/local/bin/vt
[22:45:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:45:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:45:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:45:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:45:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:45:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:45:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:45:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:53:18] This is snippy 4.6.0Show full stderr[22:53:18] This is snippy 4.6.0
[22:53:18] Written by Torsten Seemann
[22:53:18] Obtained from https://github.com/tseemann/snippy
[22:53:18] Detected operating system: linux
[22:53:18] Enabling bundled linux tools.
[22:53:18] Found bwa - /usr/local/bin/bwa
[22:53:18] Found bcftools - /usr/local/bin/bcftools
[22:53:18] Found samtools - /usr/local/bin/samtools
[22:53:18] Found java - /usr/local/bin/java
[22:53:18] Found snpEff - /usr/local/bin/snpEff
[22:53:18] Found samclip - /usr/local/bin/samclip
[22:53:18] Found seqtk - /usr/local/bin/seqtk
[22:53:18] Found parallel - /usr/local/bin/parallel
[22:53:18] Found freebayes - /usr/local/bin/freebayes
[22:53:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:53:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:53:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:53:18] Found vcfuniq - /usr/local/bin/vcfuniq
[22:53:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:53:18] Found gzip - /bin/gzip
[22:53:18] Found vt - /usr/local/bin/vt
[22:53:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:53:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:53:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:53:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:53:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:53:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:53:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:53:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:01:02] This is snippy 4.6.0Show full stderr[23:01:02] This is snippy 4.6.0
[23:01:02] Written by Torsten Seemann
[23:01:02] Obtained from https://github.com/tseemann/snippy
[23:01:02] Detected operating system: linux
[23:01:02] Enabling bundled linux tools.
[23:01:02] Found bwa - /usr/local/bin/bwa
[23:01:02] Found bcftools - /usr/local/bin/bcftools
[23:01:02] Found samtools - /usr/local/bin/samtools
[23:01:02] Found java - /usr/local/bin/java
[23:01:02] Found snpEff - /usr/local/bin/snpEff
[23:01:02] Found samclip - /usr/local/bin/samclip
[23:01:02] Found seqtk - /usr/local/bin/seqtk
[23:01:02] Found parallel - /usr/local/bin/parallel
[23:01:02] Found freebayes - /usr/local/bin/freebayes
[23:01:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:01:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:01:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:01:02] Found vcfuniq - /usr/local/bin/vcfuniq
[23:01:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:01:02] Found gzip - /bin/gzip
[23:01:02] Found vt - /usr/local/bin/vt
[23:01:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:01:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:01:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:01:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:01:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:01:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:01:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:01:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [16:12:42] This is snippy 4.6.0Show full stderr[16:12:42] This is snippy 4.6.0
[16:12:42] Written by Torsten Seemann
[16:12:42] Obtained from https://github.com/tseemann/snippy
[16:12:42] Detected operating system: linux
[16:12:42] Enabling bundled linux tools.
[16:12:42] Found bwa - /usr/local/bin/bwa
[16:12:42] Found bcftools - /usr/local/bin/bcftools
[16:12:42] Found samtools - /usr/local/bin/samtools
[16:12:42] Found java - /usr/local/bin/java
[16:12:42] Found snpEff - /usr/local/bin/snpEff
[16:12:42] Found samclip - /usr/local/bin/samclip
[16:12:42] Found seqtk - /usr/local/bin/seqtk
[16:12:42] Found parallel - /usr/local/bin/parallel
[16:12:42] Found freebayes - /usr/local/bin/freebayes
[16:12:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:12:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:12:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:12:42] Found vcfuniq - /usr/local/bin/vcfuniq
[16:12:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:12:42] Found gzip - /bin/gzip
[16:12:42] Found vt - /usr/local/bin/vt
[16:12:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:12:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:12:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:12:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:12:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:12:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:12:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:12:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:51:06] This is snippy 4.6.0Show full stderr[23:51:06] This is snippy 4.6.0
[23:51:06] Written by Torsten Seemann
[23:51:06] Obtained from https://github.com/tseemann/snippy
[23:51:06] Detected operating system: linux
[23:51:06] Enabling bundled linux tools.
[23:51:06] Found bwa - /usr/local/bin/bwa
[23:51:06] Found bcftools - /usr/local/bin/bcftools
[23:51:06] Found samtools - /usr/local/bin/samtools
[23:51:06] Found java - /usr/local/bin/java
[23:51:06] Found snpEff - /usr/local/bin/snpEff
[23:51:06] Found samclip - /usr/local/bin/samclip
[23:51:06] Found seqtk - /usr/local/bin/seqtk
[23:51:06] Found parallel - /usr/local/bin/parallel
[23:51:06] Found freebayes - /usr/local/bin/freebayes
[23:51:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:51:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:51:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:51:06] Found vcfuniq - /usr/local/bin/vcfuniq
[23:51:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:51:06] Found gzip - /bin/gzip
[23:51:06] Found vt - /usr/local/bin/vt
[23:51:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:51:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:51:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:51:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:51:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:51:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:51:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:51:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:20:27] This is snippy 4.6.0Show full stderr[21:20:27] This is snippy 4.6.0
[21:20:27] Written by Torsten Seemann
[21:20:27] Obtained from https://github.com/tseemann/snippy
[21:20:27] Detected operating system: linux
[21:20:27] Enabling bundled linux tools.
[21:20:27] Found bwa - /usr/local/bin/bwa
[21:20:27] Found bcftools - /usr/local/bin/bcftools
[21:20:27] Found samtools - /usr/local/bin/samtools
[21:20:27] Found java - /usr/local/bin/java
[21:20:27] Found snpEff - /usr/local/bin/snpEff
[21:20:27] Found samclip - /usr/local/bin/samclip
[21:20:27] Found seqtk - /usr/local/bin/seqtk
[21:20:27] Found parallel - /usr/local/bin/parallel
[21:20:27] Found freebayes - /usr/local/bin/freebayes
[21:20:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:20:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:20:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:20:27] Found vcfuniq - /usr/local/bin/vcfuniq
[21:20:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:20:27] Found gzip - /bin/gzip
[21:20:27] Found vt - /usr/local/bin/vt
[21:20:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:20:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:20:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:20:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:20:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:20:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:20:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:20:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:08:08] This is snippy 4.6.0Show full stderr[00:08:08] This is snippy 4.6.0
[00:08:08] Written by Torsten Seemann
[00:08:08] Obtained from https://github.com/tseemann/snippy
[00:08:08] Detected operating system: linux
[00:08:08] Enabling bundled linux tools.
[00:08:08] Found bwa - /usr/local/bin/bwa
[00:08:08] Found bcftools - /usr/local/bin/bcftools
[00:08:08] Found samtools - /usr/local/bin/samtools
[00:08:08] Found java - /usr/local/bin/java
[00:08:08] Found snpEff - /usr/local/bin/snpEff
[00:08:08] Found samclip - /usr/local/bin/samclip
[00:08:08] Found seqtk - /usr/local/bin/seqtk
[00:08:08] Found parallel - /usr/local/bin/parallel
[00:08:08] Found freebayes - /usr/local/bin/freebayes
[00:08:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:08:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:08:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:08:08] Found vcfuniq - /usr/local/bin/vcfuniq
[00:08:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:08:08] Found gzip - /bin/gzip
[00:08:08] Found vt - /usr/local/bin/vt
[00:08:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:08:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:08:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:08:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:08:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:08:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:08:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:08:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:44:18] This is snippy 4.6.0Show full stderr[00:44:18] This is snippy 4.6.0
[00:44:18] Written by Torsten Seemann
[00:44:18] Obtained from https://github.com/tseemann/snippy
[00:44:18] Detected operating system: linux
[00:44:18] Enabling bundled linux tools.
[00:44:18] Found bwa - /usr/local/bin/bwa
[00:44:18] Found bcftools - /usr/local/bin/bcftools
[00:44:18] Found samtools - /usr/local/bin/samtools
[00:44:18] Found java - /usr/local/bin/java
[00:44:18] Found snpEff - /usr/local/bin/snpEff
[00:44:18] Found samclip - /usr/local/bin/samclip
[00:44:18] Found seqtk - /usr/local/bin/seqtk
[00:44:18] Found parallel - /usr/local/bin/parallel
[00:44:18] Found freebayes - /usr/local/bin/freebayes
[00:44:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:44:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:44:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:44:18] Found vcfuniq - /usr/local/bin/vcfuniq
[00:44:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:44:18] Found gzip - /bin/gzip
[00:44:18] Found vt - /usr/local/bin/vt
[00:44:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:44:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:44:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:44:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:44:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:44:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:44:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:44:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:48:20] This is snippy 4.6.0Show full stderr[15:48:20] This is snippy 4.6.0
[15:48:20] Written by Torsten Seemann
[15:48:20] Obtained from https://github.com/tseemann/snippy
[15:48:20] Detected operating system: linux
[15:48:20] Enabling bundled linux tools.
[15:48:20] Found bwa - /usr/local/bin/bwa
[15:48:20] Found bcftools - /usr/local/bin/bcftools
[15:48:20] Found samtools - /usr/local/bin/samtools
[15:48:20] Found java - /usr/local/bin/java
[15:48:20] Found snpEff - /usr/local/bin/snpEff
[15:48:20] Found samclip - /usr/local/bin/samclip
[15:48:20] Found seqtk - /usr/local/bin/seqtk
[15:48:20] Found parallel - /usr/local/bin/parallel
[15:48:20] Found freebayes - /usr/local/bin/freebayes
[15:48:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:48:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:48:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:48:20] Found vcfuniq - /usr/local/bin/vcfuniq
[15:48:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:48:20] Found gzip - /bin/gzip
[15:48:20] Found vt - /usr/local/bin/vt
[15:48:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:48:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:48:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:48:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:48:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:48:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:48:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:48:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [16:44:17] This is snippy 4.6.0Show full stderr[16:44:17] This is snippy 4.6.0
[16:44:17] Written by Torsten Seemann
[16:44:17] Obtained from https://github.com/tseemann/snippy
[16:44:17] Detected operating system: linux
[16:44:17] Enabling bundled linux tools.
[16:44:17] Found bwa - /usr/local/bin/bwa
[16:44:17] Found bcftools - /usr/local/bin/bcftools
[16:44:17] Found samtools - /usr/local/bin/samtools
[16:44:17] Found java - /usr/local/bin/java
[16:44:17] Found snpEff - /usr/local/bin/snpEff
[16:44:18] Found samclip - /usr/local/bin/samclip
[16:44:18] Found seqtk - /usr/local/bin/seqtk
[16:44:18] Found parallel - /usr/local/bin/parallel
[16:44:18] Found freebayes - /usr/local/bin/freebayes
[16:44:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:44:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:44:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:44:18] Found vcfuniq - /usr/local/bin/vcfuniq
[16:44:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:44:18] Found gzip - /bin/gzip
[16:44:18] Found vt - /usr/local/bin/vt
[16:44:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:44:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:44:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:44:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:44:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:44:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:44:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:44:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:17:46] This is snippy 4.6.0Show full stderr[17:17:46] This is snippy 4.6.0
[17:17:46] Written by Torsten Seemann
[17:17:46] Obtained from https://github.com/tseemann/snippy
[17:17:46] Detected operating system: linux
[17:17:46] Enabling bundled linux tools.
[17:17:46] Found bwa - /usr/local/bin/bwa
[17:17:46] Found bcftools - /usr/local/bin/bcftools
[17:17:46] Found samtools - /usr/local/bin/samtools
[17:17:46] Found java - /usr/local/bin/java
[17:17:46] Found snpEff - /usr/local/bin/snpEff
[17:17:46] Found samclip - /usr/local/bin/samclip
[17:17:46] Found seqtk - /usr/local/bin/seqtk
[17:17:46] Found parallel - /usr/local/bin/parallel
[17:17:46] Found freebayes - /usr/local/bin/freebayes
[17:17:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:17:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:17:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:17:46] Found vcfuniq - /usr/local/bin/vcfuniq
[17:17:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:17:46] Found gzip - /bin/gzip
[17:17:46] Found vt - /usr/local/bin/vt
[17:17:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:17:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:17:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:17:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:17:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:17:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:17:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:17:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:17:42] This is snippy 4.6.0Show full stderr[18:17:42] This is snippy 4.6.0
[18:17:42] Written by Torsten Seemann
[18:17:42] Obtained from https://github.com/tseemann/snippy
[18:17:42] Detected operating system: linux
[18:17:42] Enabling bundled linux tools.
[18:17:42] Found bwa - /usr/local/bin/bwa
[18:17:42] Found bcftools - /usr/local/bin/bcftools
[18:17:42] Found samtools - /usr/local/bin/samtools
[18:17:42] Found java - /usr/local/bin/java
[18:17:42] Found snpEff - /usr/local/bin/snpEff
[18:17:42] Found samclip - /usr/local/bin/samclip
[18:17:42] Found seqtk - /usr/local/bin/seqtk
[18:17:42] Found parallel - /usr/local/bin/parallel
[18:17:42] Found freebayes - /usr/local/bin/freebayes
[18:17:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:17:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:17:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:17:42] Found vcfuniq - /usr/local/bin/vcfuniq
[18:17:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:17:42] Found gzip - /bin/gzip
[18:17:42] Found vt - /usr/local/bin/vt
[18:17:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:17:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:17:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:17:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:17:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:17:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:17:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:17:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:59:34] This is snippy 4.6.0Show full stderr[18:59:34] This is snippy 4.6.0
[18:59:34] Written by Torsten Seemann
[18:59:34] Obtained from https://github.com/tseemann/snippy
[18:59:34] Detected operating system: linux
[18:59:34] Enabling bundled linux tools.
[18:59:34] Found bwa - /usr/local/bin/bwa
[18:59:34] Found bcftools - /usr/local/bin/bcftools
[18:59:34] Found samtools - /usr/local/bin/samtools
[18:59:34] Found java - /usr/local/bin/java
[18:59:34] Found snpEff - /usr/local/bin/snpEff
[18:59:34] Found samclip - /usr/local/bin/samclip
[18:59:34] Found seqtk - /usr/local/bin/seqtk
[18:59:34] Found parallel - /usr/local/bin/parallel
[18:59:34] Found freebayes - /usr/local/bin/freebayes
[18:59:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:59:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:59:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:59:34] Found vcfuniq - /usr/local/bin/vcfuniq
[18:59:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:59:34] Found gzip - /bin/gzip
[18:59:34] Found vt - /usr/local/bin/vt
[18:59:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:59:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:59:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:59:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:59:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:59:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:59:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:59:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:33:18] This is snippy 4.6.0Show full stderr[19:33:18] This is snippy 4.6.0
[19:33:18] Written by Torsten Seemann
[19:33:18] Obtained from https://github.com/tseemann/snippy
[19:33:18] Detected operating system: linux
[19:33:18] Enabling bundled linux tools.
[19:33:18] Found bwa - /usr/local/bin/bwa
[19:33:18] Found bcftools - /usr/local/bin/bcftools
[19:33:18] Found samtools - /usr/local/bin/samtools
[19:33:18] Found java - /usr/local/bin/java
[19:33:18] Found snpEff - /usr/local/bin/snpEff
[19:33:18] Found samclip - /usr/local/bin/samclip
[19:33:18] Found seqtk - /usr/local/bin/seqtk
[19:33:18] Found parallel - /usr/local/bin/parallel
[19:33:18] Found freebayes - /usr/local/bin/freebayes
[19:33:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:33:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:33:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:33:18] Found vcfuniq - /usr/local/bin/vcfuniq
[19:33:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:33:18] Found gzip - /bin/gzip
[19:33:18] Found vt - /usr/local/bin/vt
[19:33:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:33:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:33:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:33:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:33:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:33:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:33:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:33:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:49:12] This is snippy 4.6.0Show full stderr[19:49:12] This is snippy 4.6.0
[19:49:12] Written by Torsten Seemann
[19:49:12] Obtained from https://github.com/tseemann/snippy
[19:49:12] Detected operating system: linux
[19:49:12] Enabling bundled linux tools.
[19:49:12] Found bwa - /usr/local/bin/bwa
[19:49:12] Found bcftools - /usr/local/bin/bcftools
[19:49:12] Found samtools - /usr/local/bin/samtools
[19:49:12] Found java - /usr/local/bin/java
[19:49:12] Found snpEff - /usr/local/bin/snpEff
[19:49:12] Found samclip - /usr/local/bin/samclip
[19:49:12] Found seqtk - /usr/local/bin/seqtk
[19:49:12] Found parallel - /usr/local/bin/parallel
[19:49:12] Found freebayes - /usr/local/bin/freebayes
[19:49:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:49:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:49:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:49:12] Found vcfuniq - /usr/local/bin/vcfuniq
[19:49:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:49:12] Found gzip - /bin/gzip
[19:49:12] Found vt - /usr/local/bin/vt
[19:49:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:49:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:49:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:49:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:49:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:49:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:49:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:49:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:12:18] This is snippy 4.6.0Show full stderr[21:12:18] This is snippy 4.6.0
[21:12:18] Written by Torsten Seemann
[21:12:18] Obtained from https://github.com/tseemann/snippy
[21:12:18] Detected operating system: linux
[21:12:18] Enabling bundled linux tools.
[21:12:18] Found bwa - /usr/local/bin/bwa
[21:12:18] Found bcftools - /usr/local/bin/bcftools
[21:12:18] Found samtools - /usr/local/bin/samtools
[21:12:18] Found java - /usr/local/bin/java
[21:12:18] Found snpEff - /usr/local/bin/snpEff
[21:12:18] Found samclip - /usr/local/bin/samclip
[21:12:18] Found seqtk - /usr/local/bin/seqtk
[21:12:18] Found parallel - /usr/local/bin/parallel
[21:12:18] Found freebayes - /usr/local/bin/freebayes
[21:12:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:12:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:12:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:12:18] Found vcfuniq - /usr/local/bin/vcfuniq
[21:12:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:12:18] Found gzip - /bin/gzip
[21:12:18] Found vt - /usr/local/bin/vt
[21:12:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:12:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:12:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:12:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:12:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:12:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:12:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:12:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:22:17] This is snippy 4.6.0Show full stderr[21:22:17] This is snippy 4.6.0
[21:22:17] Written by Torsten Seemann
[21:22:17] Obtained from https://github.com/tseemann/snippy
[21:22:17] Detected operating system: linux
[21:22:17] Enabling bundled linux tools.
[21:22:17] Found bwa - /usr/local/bin/bwa
[21:22:17] Found bcftools - /usr/local/bin/bcftools
[21:22:17] Found samtools - /usr/local/bin/samtools
[21:22:17] Found java - /usr/local/bin/java
[21:22:17] Found snpEff - /usr/local/bin/snpEff
[21:22:17] Found samclip - /usr/local/bin/samclip
[21:22:17] Found seqtk - /usr/local/bin/seqtk
[21:22:17] Found parallel - /usr/local/bin/parallel
[21:22:17] Found freebayes - /usr/local/bin/freebayes
[21:22:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:22:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:22:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:22:17] Found vcfuniq - /usr/local/bin/vcfuniq
[21:22:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:22:17] Found gzip - /bin/gzip
[21:22:17] Found vt - /usr/local/bin/vt
[21:22:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:22:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:22:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:22:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:22:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:22:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:22:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:22:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:03:47] This is snippy 4.6.0Show full stderr[22:03:47] This is snippy 4.6.0
[22:03:47] Written by Torsten Seemann
[22:03:47] Obtained from https://github.com/tseemann/snippy
[22:03:47] Detected operating system: linux
[22:03:47] Enabling bundled linux tools.
[22:03:48] Found bwa - /usr/local/bin/bwa
[22:03:48] Found bcftools - /usr/local/bin/bcftools
[22:03:48] Found samtools - /usr/local/bin/samtools
[22:03:48] Found java - /usr/local/bin/java
[22:03:48] Found snpEff - /usr/local/bin/snpEff
[22:03:48] Found samclip - /usr/local/bin/samclip
[22:03:48] Found seqtk - /usr/local/bin/seqtk
[22:03:48] Found parallel - /usr/local/bin/parallel
[22:03:48] Found freebayes - /usr/local/bin/freebayes
[22:03:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:03:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:03:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:03:48] Found vcfuniq - /usr/local/bin/vcfuniq
[22:03:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:03:48] Found gzip - /bin/gzip
[22:03:48] Found vt - /usr/local/bin/vt
[22:03:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:03:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:03:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:03:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:03:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:03:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:03:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:03:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:28:15] This is snippy 4.6.0Show full stderr[22:28:15] This is snippy 4.6.0
[22:28:15] Written by Torsten Seemann
[22:28:15] Obtained from https://github.com/tseemann/snippy
[22:28:15] Detected operating system: linux
[22:28:15] Enabling bundled linux tools.
[22:28:15] Found bwa - /usr/local/bin/bwa
[22:28:15] Found bcftools - /usr/local/bin/bcftools
[22:28:15] Found samtools - /usr/local/bin/samtools
[22:28:15] Found java - /usr/local/bin/java
[22:28:15] Found snpEff - /usr/local/bin/snpEff
[22:28:15] Found samclip - /usr/local/bin/samclip
[22:28:15] Found seqtk - /usr/local/bin/seqtk
[22:28:15] Found parallel - /usr/local/bin/parallel
[22:28:15] Found freebayes - /usr/local/bin/freebayes
[22:28:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:28:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:28:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:28:15] Found vcfuniq - /usr/local/bin/vcfuniq
[22:28:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:28:15] Found gzip - /bin/gzip
[22:28:15] Found vt - /usr/local/bin/vt
[22:28:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:28:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:28:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:28:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:28:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:28:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:28:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:28:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [16:05:02] This is snippy 4.6.0Show full stderr[16:05:02] This is snippy 4.6.0
[16:05:02] Written by Torsten Seemann
[16:05:02] Obtained from https://github.com/tseemann/snippy
[16:05:02] Detected operating system: linux
[16:05:02] Enabling bundled linux tools.
[16:05:02] Found bwa - /usr/local/bin/bwa
[16:05:02] Found bcftools - /usr/local/bin/bcftools
[16:05:02] Found samtools - /usr/local/bin/samtools
[16:05:02] Found java - /usr/local/bin/java
[16:05:02] Found snpEff - /usr/local/bin/snpEff
[16:05:02] Found samclip - /usr/local/bin/samclip
[16:05:02] Found seqtk - /usr/local/bin/seqtk
[16:05:02] Found parallel - /usr/local/bin/parallel
[16:05:02] Found freebayes - /usr/local/bin/freebayes
[16:05:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:05:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:05:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:05:02] Found vcfuniq - /usr/local/bin/vcfuniq
[16:05:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:05:02] Found gzip - /bin/gzip
[16:05:02] Found vt - /usr/local/bin/vt
[16:05:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:05:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:05:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:05:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:05:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:05:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:05:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:05:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [16:20:33] This is snippy 4.6.0Show full stderr[16:20:33] This is snippy 4.6.0
[16:20:33] Written by Torsten Seemann
[16:20:33] Obtained from https://github.com/tseemann/snippy
[16:20:33] Detected operating system: linux
[16:20:33] Enabling bundled linux tools.
[16:20:33] Found bwa - /usr/local/bin/bwa
[16:20:33] Found bcftools - /usr/local/bin/bcftools
[16:20:33] Found samtools - /usr/local/bin/samtools
[16:20:33] Found java - /usr/local/bin/java
[16:20:33] Found snpEff - /usr/local/bin/snpEff
[16:20:33] Found samclip - /usr/local/bin/samclip
[16:20:33] Found seqtk - /usr/local/bin/seqtk
[16:20:33] Found parallel - /usr/local/bin/parallel
[16:20:33] Found freebayes - /usr/local/bin/freebayes
[16:20:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[16:20:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[16:20:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[16:20:33] Found vcfuniq - /usr/local/bin/vcfuniq
[16:20:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[16:20:33] Found gzip - /bin/gzip
[16:20:33] Found vt - /usr/local/bin/vt
[16:20:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[16:20:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[16:20:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[16:20:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[16:20:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[16:20:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[16:20:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[16:20:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:01] This is snippy 4.6.0Show full stderr[17:26:01] This is snippy 4.6.0
[17:26:01] Written by Torsten Seemann
[17:26:01] Obtained from https://github.com/tseemann/snippy
[17:26:01] Detected operating system: linux
[17:26:01] Enabling bundled linux tools.
[17:26:01] Found bwa - /usr/local/bin/bwa
[17:26:01] Found bcftools - /usr/local/bin/bcftools
[17:26:01] Found samtools - /usr/local/bin/samtools
[17:26:01] Found java - /usr/local/bin/java
[17:26:01] Found snpEff - /usr/local/bin/snpEff
[17:26:01] Found samclip - /usr/local/bin/samclip
[17:26:01] Found seqtk - /usr/local/bin/seqtk
[17:26:01] Found parallel - /usr/local/bin/parallel
[17:26:01] Found freebayes - /usr/local/bin/freebayes
[17:26:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:01] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:01] Found gzip - /bin/gzip
[17:26:01] Found vt - /usr/local/bin/vt
[17:26:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:01:17] This is snippy 4.6.0Show full stderr[18:01:17] This is snippy 4.6.0
[18:01:17] Written by Torsten Seemann
[18:01:17] Obtained from https://github.com/tseemann/snippy
[18:01:17] Detected operating system: linux
[18:01:17] Enabling bundled linux tools.
[18:01:17] Found bwa - /usr/local/bin/bwa
[18:01:17] Found bcftools - /usr/local/bin/bcftools
[18:01:17] Found samtools - /usr/local/bin/samtools
[18:01:17] Found java - /usr/local/bin/java
[18:01:17] Found snpEff - /usr/local/bin/snpEff
[18:01:17] Found samclip - /usr/local/bin/samclip
[18:01:17] Found seqtk - /usr/local/bin/seqtk
[18:01:17] Found parallel - /usr/local/bin/parallel
[18:01:17] Found freebayes - /usr/local/bin/freebayes
[18:01:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:01:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:01:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:01:17] Found vcfuniq - /usr/local/bin/vcfuniq
[18:01:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:01:17] Found gzip - /bin/gzip
[18:01:17] Found vt - /usr/local/bin/vt
[18:01:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:01:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:01:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:01:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:01:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:01:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:01:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:01:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:26:27] This is snippy 4.6.0Show full stderr[18:26:27] This is snippy 4.6.0
[18:26:27] Written by Torsten Seemann
[18:26:27] Obtained from https://github.com/tseemann/snippy
[18:26:27] Detected operating system: linux
[18:26:27] Enabling bundled linux tools.
[18:26:27] Found bwa - /usr/local/bin/bwa
[18:26:27] Found bcftools - /usr/local/bin/bcftools
[18:26:27] Found samtools - /usr/local/bin/samtools
[18:26:27] Found java - /usr/local/bin/java
[18:26:27] Found snpEff - /usr/local/bin/snpEff
[18:26:27] Found samclip - /usr/local/bin/samclip
[18:26:27] Found seqtk - /usr/local/bin/seqtk
[18:26:27] Found parallel - /usr/local/bin/parallel
[18:26:27] Found freebayes - /usr/local/bin/freebayes
[18:26:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:26:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:26:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:26:27] Found vcfuniq - /usr/local/bin/vcfuniq
[18:26:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:26:27] Found gzip - /bin/gzip
[18:26:27] Found vt - /usr/local/bin/vt
[18:26:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:26:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:26:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:26:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:26:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:26:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:26:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:26:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:16:59] This is snippy 4.6.0Show full stderr[17:16:59] This is snippy 4.6.0
[17:16:59] Written by Torsten Seemann
[17:16:59] Obtained from https://github.com/tseemann/snippy
[17:16:59] Detected operating system: linux
[17:16:59] Enabling bundled linux tools.
[17:16:59] Found bwa - /usr/local/bin/bwa
[17:16:59] Found bcftools - /usr/local/bin/bcftools
[17:16:59] Found samtools - /usr/local/bin/samtools
[17:16:59] Found java - /usr/local/bin/java
[17:16:59] Found snpEff - /usr/local/bin/snpEff
[17:16:59] Found samclip - /usr/local/bin/samclip
[17:16:59] Found seqtk - /usr/local/bin/seqtk
[17:16:59] Found parallel - /usr/local/bin/parallel
[17:16:59] Found freebayes - /usr/local/bin/freebayes
[17:16:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:16:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:16:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:16:59] Found vcfuniq - /usr/local/bin/vcfuniq
[17:16:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:16:59] Found gzip - /bin/gzip
[17:16:59] Found vt - /usr/local/bin/vt
[17:16:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:16:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:16:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:16:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:16:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:17:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:17:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:17:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:43:18] This is snippy 4.6.0Show full stderr[18:43:18] This is snippy 4.6.0
[18:43:18] Written by Torsten Seemann
[18:43:18] Obtained from https://github.com/tseemann/snippy
[18:43:18] Detected operating system: linux
[18:43:18] Enabling bundled linux tools.
[18:43:18] Found bwa - /usr/local/bin/bwa
[18:43:18] Found bcftools - /usr/local/bin/bcftools
[18:43:18] Found samtools - /usr/local/bin/samtools
[18:43:18] Found java - /usr/local/bin/java
[18:43:18] Found snpEff - /usr/local/bin/snpEff
[18:43:18] Found samclip - /usr/local/bin/samclip
[18:43:18] Found seqtk - /usr/local/bin/seqtk
[18:43:18] Found parallel - /usr/local/bin/parallel
[18:43:18] Found freebayes - /usr/local/bin/freebayes
[18:43:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:43:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:43:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:43:18] Found vcfuniq - /usr/local/bin/vcfuniq
[18:43:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:43:18] Found gzip - /bin/gzip
[18:43:18] Found vt - /usr/local/bin/vt
[18:43:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:43:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:43:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:43:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:43:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:43:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:43:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:43:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:59:04] This is snippy 4.6.0Show full stderr[18:59:04] This is snippy 4.6.0
[18:59:04] Written by Torsten Seemann
[18:59:04] Obtained from https://github.com/tseemann/snippy
[18:59:04] Detected operating system: linux
[18:59:04] Enabling bundled linux tools.
[18:59:04] Found bwa - /usr/local/bin/bwa
[18:59:04] Found bcftools - /usr/local/bin/bcftools
[18:59:04] Found samtools - /usr/local/bin/samtools
[18:59:04] Found java - /usr/local/bin/java
[18:59:04] Found snpEff - /usr/local/bin/snpEff
[18:59:04] Found samclip - /usr/local/bin/samclip
[18:59:04] Found seqtk - /usr/local/bin/seqtk
[18:59:04] Found parallel - /usr/local/bin/parallel
[18:59:04] Found freebayes - /usr/local/bin/freebayes
[18:59:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:59:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:59:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:59:04] Found vcfuniq - /usr/local/bin/vcfuniq
[18:59:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:59:04] Found gzip - /bin/gzip
[18:59:04] Found vt - /usr/local/bin/vt
[18:59:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:59:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:59:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:59:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:59:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:59:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:59:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:59:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:59:19] This is snippy 4.6.0Show full stderr[18:59:19] This is snippy 4.6.0
[18:59:19] Written by Torsten Seemann
[18:59:19] Obtained from https://github.com/tseemann/snippy
[18:59:19] Detected operating system: linux
[18:59:19] Enabling bundled linux tools.
[18:59:19] Found bwa - /usr/local/bin/bwa
[18:59:19] Found bcftools - /usr/local/bin/bcftools
[18:59:19] Found samtools - /usr/local/bin/samtools
[18:59:19] Found java - /usr/local/bin/java
[18:59:19] Found snpEff - /usr/local/bin/snpEff
[18:59:19] Found samclip - /usr/local/bin/samclip
[18:59:19] Found seqtk - /usr/local/bin/seqtk
[18:59:19] Found parallel - /usr/local/bin/parallel
[18:59:19] Found freebayes - /usr/local/bin/freebayes
[18:59:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:59:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:59:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:59:19] Found vcfuniq - /usr/local/bin/vcfuniq
[18:59:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:59:19] Found gzip - /bin/gzip
[18:59:19] Found vt - /usr/local/bin/vt
[18:59:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:59:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:59:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:59:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:59:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:59:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:59:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:59:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:07:46] This is snippy 4.6.0Show full stderr[19:07:46] This is snippy 4.6.0
[19:07:46] Written by Torsten Seemann
[19:07:46] Obtained from https://github.com/tseemann/snippy
[19:07:46] Detected operating system: linux
[19:07:46] Enabling bundled linux tools.
[19:07:46] Found bwa - /usr/local/bin/bwa
[19:07:46] Found bcftools - /usr/local/bin/bcftools
[19:07:46] Found samtools - /usr/local/bin/samtools
[19:07:46] Found java - /usr/local/bin/java
[19:07:46] Found snpEff - /usr/local/bin/snpEff
[19:07:46] Found samclip - /usr/local/bin/samclip
[19:07:46] Found seqtk - /usr/local/bin/seqtk
[19:07:46] Found parallel - /usr/local/bin/parallel
[19:07:46] Found freebayes - /usr/local/bin/freebayes
[19:07:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:07:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:07:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:07:46] Found vcfuniq - /usr/local/bin/vcfuniq
[19:07:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:07:46] Found gzip - /bin/gzip
[19:07:46] Found vt - /usr/local/bin/vt
[19:07:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:07:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:07:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:07:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:07:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:07:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:07:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:07:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:24:31] This is snippy 4.6.0Show full stderr[19:24:31] This is snippy 4.6.0
[19:24:31] Written by Torsten Seemann
[19:24:31] Obtained from https://github.com/tseemann/snippy
[19:24:31] Detected operating system: linux
[19:24:31] Enabling bundled linux tools.
[19:24:31] Found bwa - /usr/local/bin/bwa
[19:24:31] Found bcftools - /usr/local/bin/bcftools
[19:24:31] Found samtools - /usr/local/bin/samtools
[19:24:31] Found java - /usr/local/bin/java
[19:24:31] Found snpEff - /usr/local/bin/snpEff
[19:24:31] Found samclip - /usr/local/bin/samclip
[19:24:32] Found seqtk - /usr/local/bin/seqtk
[19:24:32] Found parallel - /usr/local/bin/parallel
[19:24:32] Found freebayes - /usr/local/bin/freebayes
[19:24:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:24:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:24:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:24:32] Found vcfuniq - /usr/local/bin/vcfuniq
[19:24:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:24:32] Found gzip - /bin/gzip
[19:24:32] Found vt - /usr/local/bin/vt
[19:24:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:24:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:24:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:24:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:24:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:24:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:24:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:24:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:48:57] This is snippy 4.6.0Show full stderr[19:48:57] This is snippy 4.6.0
[19:48:57] Written by Torsten Seemann
[19:48:57] Obtained from https://github.com/tseemann/snippy
[19:48:57] Detected operating system: linux
[19:48:57] Enabling bundled linux tools.
[19:48:57] Found bwa - /usr/local/bin/bwa
[19:48:57] Found bcftools - /usr/local/bin/bcftools
[19:48:57] Found samtools - /usr/local/bin/samtools
[19:48:57] Found java - /usr/local/bin/java
[19:48:57] Found snpEff - /usr/local/bin/snpEff
[19:48:57] Found samclip - /usr/local/bin/samclip
[19:48:57] Found seqtk - /usr/local/bin/seqtk
[19:48:57] Found parallel - /usr/local/bin/parallel
[19:48:57] Found freebayes - /usr/local/bin/freebayes
[19:48:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:48:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:48:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:48:57] Found vcfuniq - /usr/local/bin/vcfuniq
[19:48:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:48:57] Found gzip - /bin/gzip
[19:48:57] Found vt - /usr/local/bin/vt
[19:48:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:48:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:48:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:48:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:48:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:48:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:48:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:48:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:18:12] This is snippy 4.6.0Show full stderr[18:18:12] This is snippy 4.6.0
[18:18:12] Written by Torsten Seemann
[18:18:12] Obtained from https://github.com/tseemann/snippy
[18:18:12] Detected operating system: linux
[18:18:12] Enabling bundled linux tools.
[18:18:13] Found bwa - /usr/local/bin/bwa
[18:18:13] Found bcftools - /usr/local/bin/bcftools
[18:18:13] Found samtools - /usr/local/bin/samtools
[18:18:13] Found java - /usr/local/bin/java
[18:18:13] Found snpEff - /usr/local/bin/snpEff
[18:18:13] Found samclip - /usr/local/bin/samclip
[18:18:13] Found seqtk - /usr/local/bin/seqtk
[18:18:13] Found parallel - /usr/local/bin/parallel
[18:18:13] Found freebayes - /usr/local/bin/freebayes
[18:18:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:18:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:18:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:18:13] Found vcfuniq - /usr/local/bin/vcfuniq
[18:18:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:18:13] Found gzip - /bin/gzip
[18:18:13] Found vt - /usr/local/bin/vt
[18:18:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:18:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:18:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:18:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:18:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:18:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:18:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:18:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:26:44] This is snippy 4.6.0Show full stderr[18:26:44] This is snippy 4.6.0
[18:26:44] Written by Torsten Seemann
[18:26:44] Obtained from https://github.com/tseemann/snippy
[18:26:44] Detected operating system: linux
[18:26:44] Enabling bundled linux tools.
[18:26:44] Found bwa - /usr/local/bin/bwa
[18:26:44] Found bcftools - /usr/local/bin/bcftools
[18:26:44] Found samtools - /usr/local/bin/samtools
[18:26:44] Found java - /usr/local/bin/java
[18:26:44] Found snpEff - /usr/local/bin/snpEff
[18:26:44] Found samclip - /usr/local/bin/samclip
[18:26:44] Found seqtk - /usr/local/bin/seqtk
[18:26:44] Found parallel - /usr/local/bin/parallel
[18:26:44] Found freebayes - /usr/local/bin/freebayes
[18:26:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:26:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:26:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:26:44] Found vcfuniq - /usr/local/bin/vcfuniq
[18:26:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:26:44] Found gzip - /bin/gzip
[18:26:44] Found vt - /usr/local/bin/vt
[18:26:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:26:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:26:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:26:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:26:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:26:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:26:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:26:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:27:18] This is snippy 4.6.0Show full stderr[18:27:18] This is snippy 4.6.0
[18:27:18] Written by Torsten Seemann
[18:27:18] Obtained from https://github.com/tseemann/snippy
[18:27:18] Detected operating system: linux
[18:27:18] Enabling bundled linux tools.
[18:27:18] Found bwa - /usr/local/bin/bwa
[18:27:18] Found bcftools - /usr/local/bin/bcftools
[18:27:19] Found samtools - /usr/local/bin/samtools
[18:27:19] Found java - /usr/local/bin/java
[18:27:19] Found snpEff - /usr/local/bin/snpEff
[18:27:19] Found samclip - /usr/local/bin/samclip
[18:27:19] Found seqtk - /usr/local/bin/seqtk
[18:27:19] Found parallel - /usr/local/bin/parallel
[18:27:19] Found freebayes - /usr/local/bin/freebayes
[18:27:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:27:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:27:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:27:19] Found vcfuniq - /usr/local/bin/vcfuniq
[18:27:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:27:19] Found gzip - /bin/gzip
[18:27:19] Found vt - /usr/local/bin/vt
[18:27:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:27:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:27:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:27:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:27:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:27:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:27:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:27:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:35:18] This is snippy 4.6.0Show full stderr[18:35:18] This is snippy 4.6.0
[18:35:18] Written by Torsten Seemann
[18:35:18] Obtained from https://github.com/tseemann/snippy
[18:35:18] Detected operating system: linux
[18:35:18] Enabling bundled linux tools.
[18:35:18] Found bwa - /usr/local/bin/bwa
[18:35:18] Found bcftools - /usr/local/bin/bcftools
[18:35:18] Found samtools - /usr/local/bin/samtools
[18:35:18] Found java - /usr/local/bin/java
[18:35:18] Found snpEff - /usr/local/bin/snpEff
[18:35:18] Found samclip - /usr/local/bin/samclip
[18:35:18] Found seqtk - /usr/local/bin/seqtk
[18:35:18] Found parallel - /usr/local/bin/parallel
[18:35:18] Found freebayes - /usr/local/bin/freebayes
[18:35:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:35:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:35:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:35:18] Found vcfuniq - /usr/local/bin/vcfuniq
[18:35:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:35:18] Found gzip - /bin/gzip
[18:35:18] Found vt - /usr/local/bin/vt
[18:35:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:35:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:35:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:35:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:35:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:35:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:35:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:35:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:59:48] This is snippy 4.6.0Show full stderr[18:59:48] This is snippy 4.6.0
[18:59:48] Written by Torsten Seemann
[18:59:48] Obtained from https://github.com/tseemann/snippy
[18:59:48] Detected operating system: linux
[18:59:48] Enabling bundled linux tools.
[18:59:48] Found bwa - /usr/local/bin/bwa
[18:59:48] Found bcftools - /usr/local/bin/bcftools
[18:59:48] Found samtools - /usr/local/bin/samtools
[18:59:48] Found java - /usr/local/bin/java
[18:59:48] Found snpEff - /usr/local/bin/snpEff
[18:59:48] Found samclip - /usr/local/bin/samclip
[18:59:48] Found seqtk - /usr/local/bin/seqtk
[18:59:48] Found parallel - /usr/local/bin/parallel
[18:59:48] Found freebayes - /usr/local/bin/freebayes
[18:59:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:59:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:59:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:59:48] Found vcfuniq - /usr/local/bin/vcfuniq
[18:59:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:59:48] Found gzip - /bin/gzip
[18:59:48] Found vt - /usr/local/bin/vt
[18:59:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:59:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:59:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:59:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:59:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:59:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:59:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:59:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:08:18] This is snippy 4.6.0Show full stderr[19:08:18] This is snippy 4.6.0
[19:08:18] Written by Torsten Seemann
[19:08:18] Obtained from https://github.com/tseemann/snippy
[19:08:18] Detected operating system: linux
[19:08:18] Enabling bundled linux tools.
[19:08:18] Found bwa - /usr/local/bin/bwa
[19:08:18] Found bcftools - /usr/local/bin/bcftools
[19:08:18] Found samtools - /usr/local/bin/samtools
[19:08:18] Found java - /usr/local/bin/java
[19:08:18] Found snpEff - /usr/local/bin/snpEff
[19:08:18] Found samclip - /usr/local/bin/samclip
[19:08:18] Found seqtk - /usr/local/bin/seqtk
[19:08:18] Found parallel - /usr/local/bin/parallel
[19:08:18] Found freebayes - /usr/local/bin/freebayes
[19:08:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:08:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:08:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:08:18] Found vcfuniq - /usr/local/bin/vcfuniq
[19:08:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:08:18] Found gzip - /bin/gzip
[19:08:18] Found vt - /usr/local/bin/vt
[19:08:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:08:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:08:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:08:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:08:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:08:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:08:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:08:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:16:18] This is snippy 4.6.0Show full stderr[19:16:18] This is snippy 4.6.0
[19:16:18] Written by Torsten Seemann
[19:16:18] Obtained from https://github.com/tseemann/snippy
[19:16:18] Detected operating system: linux
[19:16:18] Enabling bundled linux tools.
[19:16:18] Found bwa - /usr/local/bin/bwa
[19:16:18] Found bcftools - /usr/local/bin/bcftools
[19:16:18] Found samtools - /usr/local/bin/samtools
[19:16:18] Found java - /usr/local/bin/java
[19:16:18] Found snpEff - /usr/local/bin/snpEff
[19:16:18] Found samclip - /usr/local/bin/samclip
[19:16:18] Found seqtk - /usr/local/bin/seqtk
[19:16:18] Found parallel - /usr/local/bin/parallel
[19:16:18] Found freebayes - /usr/local/bin/freebayes
[19:16:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:16:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:16:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:16:18] Found vcfuniq - /usr/local/bin/vcfuniq
[19:16:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:16:18] Found gzip - /bin/gzip
[19:16:18] Found vt - /usr/local/bin/vt
[19:16:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:16:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:16:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:16:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:16:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:16:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:16:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:16:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:25:18] This is snippy 4.6.0Show full stderr[19:25:18] This is snippy 4.6.0
[19:25:18] Written by Torsten Seemann
[19:25:18] Obtained from https://github.com/tseemann/snippy
[19:25:18] Detected operating system: linux
[19:25:18] Enabling bundled linux tools.
[19:25:18] Found bwa - /usr/local/bin/bwa
[19:25:18] Found bcftools - /usr/local/bin/bcftools
[19:25:18] Found samtools - /usr/local/bin/samtools
[19:25:18] Found java - /usr/local/bin/java
[19:25:18] Found snpEff - /usr/local/bin/snpEff
[19:25:18] Found samclip - /usr/local/bin/samclip
[19:25:18] Found seqtk - /usr/local/bin/seqtk
[19:25:18] Found parallel - /usr/local/bin/parallel
[19:25:18] Found freebayes - /usr/local/bin/freebayes
[19:25:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:25:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:25:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:25:18] Found vcfuniq - /usr/local/bin/vcfuniq
[19:25:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:25:18] Found gzip - /bin/gzip
[19:25:18] Found vt - /usr/local/bin/vt
[19:25:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:25:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:25:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:25:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:25:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:25:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:25:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:25:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:40:57] This is snippy 4.6.0Show full stderr[19:40:57] This is snippy 4.6.0
[19:40:57] Written by Torsten Seemann
[19:40:57] Obtained from https://github.com/tseemann/snippy
[19:40:57] Detected operating system: linux
[19:40:57] Enabling bundled linux tools.
[19:40:57] Found bwa - /usr/local/bin/bwa
[19:40:57] Found bcftools - /usr/local/bin/bcftools
[19:40:57] Found samtools - /usr/local/bin/samtools
[19:40:58] Found java - /usr/local/bin/java
[19:40:58] Found snpEff - /usr/local/bin/snpEff
[19:40:58] Found samclip - /usr/local/bin/samclip
[19:40:58] Found seqtk - /usr/local/bin/seqtk
[19:40:58] Found parallel - /usr/local/bin/parallel
[19:40:58] Found freebayes - /usr/local/bin/freebayes
[19:40:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:40:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:40:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:40:58] Found vcfuniq - /usr/local/bin/vcfuniq
[19:40:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:40:58] Found gzip - /bin/gzip
[19:40:58] Found vt - /usr/local/bin/vt
[19:40:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:40:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:40:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:40:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:40:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:40:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:40:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:40:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:41:18] This is snippy 4.6.0Show full stderr[19:41:18] This is snippy 4.6.0
[19:41:18] Written by Torsten Seemann
[19:41:18] Obtained from https://github.com/tseemann/snippy
[19:41:18] Detected operating system: linux
[19:41:18] Enabling bundled linux tools.
[19:41:18] Found bwa - /usr/local/bin/bwa
[19:41:18] Found bcftools - /usr/local/bin/bcftools
[19:41:18] Found samtools - /usr/local/bin/samtools
[19:41:18] Found java - /usr/local/bin/java
[19:41:18] Found snpEff - /usr/local/bin/snpEff
[19:41:18] Found samclip - /usr/local/bin/samclip
[19:41:18] Found seqtk - /usr/local/bin/seqtk
[19:41:18] Found parallel - /usr/local/bin/parallel
[19:41:18] Found freebayes - /usr/local/bin/freebayes
[19:41:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:41:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:41:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:41:18] Found vcfuniq - /usr/local/bin/vcfuniq
[19:41:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:41:18] Found gzip - /bin/gzip
[19:41:18] Found vt - /usr/local/bin/vt
[19:41:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:41:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:41:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:41:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:41:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:41:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:41:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:41:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:48:58] This is snippy 4.6.0Show full stderr[19:48:58] This is snippy 4.6.0
[19:48:58] Written by Torsten Seemann
[19:48:58] Obtained from https://github.com/tseemann/snippy
[19:48:58] Detected operating system: linux
[19:48:58] Enabling bundled linux tools.
[19:48:58] Found bwa - /usr/local/bin/bwa
[19:48:58] Found bcftools - /usr/local/bin/bcftools
[19:48:58] Found samtools - /usr/local/bin/samtools
[19:48:58] Found java - /usr/local/bin/java
[19:48:58] Found snpEff - /usr/local/bin/snpEff
[19:48:58] Found samclip - /usr/local/bin/samclip
[19:48:58] Found seqtk - /usr/local/bin/seqtk
[19:48:58] Found parallel - /usr/local/bin/parallel
[19:48:58] Found freebayes - /usr/local/bin/freebayes
[19:48:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:48:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:48:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:48:58] Found vcfuniq - /usr/local/bin/vcfuniq
[19:48:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:48:58] Found gzip - /bin/gzip
[19:48:58] Found vt - /usr/local/bin/vt
[19:48:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:48:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:48:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:48:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:48:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:48:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:48:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:48:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:13:46] This is snippy 4.6.0Show full stderr[20:13:46] This is snippy 4.6.0
[20:13:46] Written by Torsten Seemann
[20:13:46] Obtained from https://github.com/tseemann/snippy
[20:13:46] Detected operating system: linux
[20:13:46] Enabling bundled linux tools.
[20:13:46] Found bwa - /usr/local/bin/bwa
[20:13:46] Found bcftools - /usr/local/bin/bcftools
[20:13:46] Found samtools - /usr/local/bin/samtools
[20:13:46] Found java - /usr/local/bin/java
[20:13:46] Found snpEff - /usr/local/bin/snpEff
[20:13:46] Found samclip - /usr/local/bin/samclip
[20:13:46] Found seqtk - /usr/local/bin/seqtk
[20:13:46] Found parallel - /usr/local/bin/parallel
[20:13:46] Found freebayes - /usr/local/bin/freebayes
[20:13:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:13:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:13:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:13:46] Found vcfuniq - /usr/local/bin/vcfuniq
[20:13:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:13:46] Found gzip - /bin/gzip
[20:13:46] Found vt - /usr/local/bin/vt
[20:13:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:13:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:13:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:13:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:13:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:13:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:13:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:13:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:14:15] This is snippy 4.6.0Show full stderr[20:14:15] This is snippy 4.6.0
[20:14:15] Written by Torsten Seemann
[20:14:15] Obtained from https://github.com/tseemann/snippy
[20:14:15] Detected operating system: linux
[20:14:15] Enabling bundled linux tools.
[20:14:15] Found bwa - /usr/local/bin/bwa
[20:14:15] Found bcftools - /usr/local/bin/bcftools
[20:14:15] Found samtools - /usr/local/bin/samtools
[20:14:15] Found java - /usr/local/bin/java
[20:14:15] Found snpEff - /usr/local/bin/snpEff
[20:14:15] Found samclip - /usr/local/bin/samclip
[20:14:15] Found seqtk - /usr/local/bin/seqtk
[20:14:15] Found parallel - /usr/local/bin/parallel
[20:14:15] Found freebayes - /usr/local/bin/freebayes
[20:14:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:14:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:14:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:14:15] Found vcfuniq - /usr/local/bin/vcfuniq
[20:14:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:14:15] Found gzip - /bin/gzip
[20:14:15] Found vt - /usr/local/bin/vt
[20:14:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:14:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:14:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:14:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:14:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:14:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:14:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:14:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [15:56:26] This is snippy 4.6.0Show full stderr[15:56:26] This is snippy 4.6.0
[15:56:26] Written by Torsten Seemann
[15:56:26] Obtained from https://github.com/tseemann/snippy
[15:56:26] Detected operating system: linux
[15:56:26] Enabling bundled linux tools.
[15:56:26] Found bwa - /usr/local/bin/bwa
[15:56:26] Found bcftools - /usr/local/bin/bcftools
[15:56:26] Found samtools - /usr/local/bin/samtools
[15:56:26] Found java - /usr/local/bin/java
[15:56:26] Found snpEff - /usr/local/bin/snpEff
[15:56:26] Found samclip - /usr/local/bin/samclip
[15:56:26] Found seqtk - /usr/local/bin/seqtk
[15:56:26] Found parallel - /usr/local/bin/parallel
[15:56:26] Found freebayes - /usr/local/bin/freebayes
[15:56:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:56:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:56:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:56:26] Found vcfuniq - /usr/local/bin/vcfuniq
[15:56:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:56:26] Found gzip - /bin/gzip
[15:56:26] Found vt - /usr/local/bin/vt
[15:56:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:56:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:56:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:56:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:56:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:56:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:56:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:56:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:22:49] This is snippy 4.6.0Show full stderr[20:22:49] This is snippy 4.6.0
[20:22:49] Written by Torsten Seemann
[20:22:49] Obtained from https://github.com/tseemann/snippy
[20:22:49] Detected operating system: linux
[20:22:49] Enabling bundled linux tools.
[20:22:49] Found bwa - /usr/local/bin/bwa
[20:22:49] Found bcftools - /usr/local/bin/bcftools
[20:22:49] Found samtools - /usr/local/bin/samtools
[20:22:49] Found java - /usr/local/bin/java
[20:22:49] Found snpEff - /usr/local/bin/snpEff
[20:22:49] Found samclip - /usr/local/bin/samclip
[20:22:49] Found seqtk - /usr/local/bin/seqtk
[20:22:49] Found parallel - /usr/local/bin/parallel
[20:22:49] Found freebayes - /usr/local/bin/freebayes
[20:22:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:22:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:22:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:22:49] Found vcfuniq - /usr/local/bin/vcfuniq
[20:22:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:22:49] Found gzip - /bin/gzip
[20:22:49] Found vt - /usr/local/bin/vt
[20:22:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:22:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:22:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:22:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:22:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:22:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:22:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:22:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:05:48] This is snippy 4.6.0Show full stderr[20:05:48] This is snippy 4.6.0
[20:05:48] Written by Torsten Seemann
[20:05:48] Obtained from https://github.com/tseemann/snippy
[20:05:48] Detected operating system: linux
[20:05:48] Enabling bundled linux tools.
[20:05:48] Found bwa - /usr/local/bin/bwa
[20:05:48] Found bcftools - /usr/local/bin/bcftools
[20:05:48] Found samtools - /usr/local/bin/samtools
[20:05:48] Found java - /usr/local/bin/java
[20:05:48] Found snpEff - /usr/local/bin/snpEff
[20:05:48] Found samclip - /usr/local/bin/samclip
[20:05:48] Found seqtk - /usr/local/bin/seqtk
[20:05:48] Found parallel - /usr/local/bin/parallel
[20:05:48] Found freebayes - /usr/local/bin/freebayes
[20:05:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:05:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:05:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:05:48] Found vcfuniq - /usr/local/bin/vcfuniq
[20:05:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:05:48] Found gzip - /bin/gzip
[20:05:48] Found vt - /usr/local/bin/vt
[20:05:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:05:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:05:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:05:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:05:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:05:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:05:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:05:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:45:17] This is snippy 4.6.0Show full stderr[00:45:17] This is snippy 4.6.0
[00:45:17] Written by Torsten Seemann
[00:45:17] Obtained from https://github.com/tseemann/snippy
[00:45:17] Detected operating system: linux
[00:45:17] Enabling bundled linux tools.
[00:45:17] Found bwa - /usr/local/bin/bwa
[00:45:17] Found bcftools - /usr/local/bin/bcftools
[00:45:17] Found samtools - /usr/local/bin/samtools
[00:45:17] Found java - /usr/local/bin/java
[00:45:17] Found snpEff - /usr/local/bin/snpEff
[00:45:17] Found samclip - /usr/local/bin/samclip
[00:45:17] Found seqtk - /usr/local/bin/seqtk
[00:45:17] Found parallel - /usr/local/bin/parallel
[00:45:17] Found freebayes - /usr/local/bin/freebayes
[00:45:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:45:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:45:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:45:17] Found vcfuniq - /usr/local/bin/vcfuniq
[00:45:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:45:17] Found gzip - /bin/gzip
[00:45:17] Found vt - /usr/local/bin/vt
[00:45:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:45:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:45:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:45:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:45:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:45:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:45:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:45:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:01:17] This is snippy 4.6.0Show full stderr[01:01:17] This is snippy 4.6.0
[01:01:17] Written by Torsten Seemann
[01:01:17] Obtained from https://github.com/tseemann/snippy
[01:01:17] Detected operating system: linux
[01:01:17] Enabling bundled linux tools.
[01:01:17] Found bwa - /usr/local/bin/bwa
[01:01:17] Found bcftools - /usr/local/bin/bcftools
[01:01:17] Found samtools - /usr/local/bin/samtools
[01:01:17] Found java - /usr/local/bin/java
[01:01:17] Found snpEff - /usr/local/bin/snpEff
[01:01:17] Found samclip - /usr/local/bin/samclip
[01:01:17] Found seqtk - /usr/local/bin/seqtk
[01:01:17] Found parallel - /usr/local/bin/parallel
[01:01:17] Found freebayes - /usr/local/bin/freebayes
[01:01:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:01:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:01:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:01:17] Found vcfuniq - /usr/local/bin/vcfuniq
[01:01:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:01:17] Found gzip - /bin/gzip
[01:01:17] Found vt - /usr/local/bin/vt
[01:01:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:01:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:01:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:01:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:01:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:01:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:01:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:01:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:17:40] This is snippy 4.6.0Show full stderr[01:17:40] This is snippy 4.6.0
[01:17:40] Written by Torsten Seemann
[01:17:40] Obtained from https://github.com/tseemann/snippy
[01:17:40] Detected operating system: linux
[01:17:40] Enabling bundled linux tools.
[01:17:40] Found bwa - /usr/local/bin/bwa
[01:17:40] Found bcftools - /usr/local/bin/bcftools
[01:17:40] Found samtools - /usr/local/bin/samtools
[01:17:40] Found java - /usr/local/bin/java
[01:17:40] Found snpEff - /usr/local/bin/snpEff
[01:17:40] Found samclip - /usr/local/bin/samclip
[01:17:40] Found seqtk - /usr/local/bin/seqtk
[01:17:40] Found parallel - /usr/local/bin/parallel
[01:17:40] Found freebayes - /usr/local/bin/freebayes
[01:17:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:17:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:17:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:17:40] Found vcfuniq - /usr/local/bin/vcfuniq
[01:17:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:17:40] Found gzip - /bin/gzip
[01:17:40] Found vt - /usr/local/bin/vt
[01:17:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:17:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:17:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:17:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:17:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:17:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:17:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:17:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:14:30] This is snippy 4.6.0Show full stderr[20:14:30] This is snippy 4.6.0
[20:14:30] Written by Torsten Seemann
[20:14:30] Obtained from https://github.com/tseemann/snippy
[20:14:30] Detected operating system: linux
[20:14:30] Enabling bundled linux tools.
[20:14:30] Found bwa - /usr/local/bin/bwa
[20:14:30] Found bcftools - /usr/local/bin/bcftools
[20:14:30] Found samtools - /usr/local/bin/samtools
[20:14:30] Found java - /usr/local/bin/java
[20:14:30] Found snpEff - /usr/local/bin/snpEff
[20:14:30] Found samclip - /usr/local/bin/samclip
[20:14:30] Found seqtk - /usr/local/bin/seqtk
[20:14:30] Found parallel - /usr/local/bin/parallel
[20:14:30] Found freebayes - /usr/local/bin/freebayes
[20:14:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:14:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:14:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:14:30] Found vcfuniq - /usr/local/bin/vcfuniq
[20:14:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:14:30] Found gzip - /bin/gzip
[20:14:30] Found vt - /usr/local/bin/vt
[20:14:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:14:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:14:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:14:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:14:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:14:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:14:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:14:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:26:47] This is snippy 4.6.0Show full stderr[01:26:47] This is snippy 4.6.0
[01:26:47] Written by Torsten Seemann
[01:26:47] Obtained from https://github.com/tseemann/snippy
[01:26:47] Detected operating system: linux
[01:26:47] Enabling bundled linux tools.
[01:26:47] Found bwa - /usr/local/bin/bwa
[01:26:47] Found bcftools - /usr/local/bin/bcftools
[01:26:47] Found samtools - /usr/local/bin/samtools
[01:26:47] Found java - /usr/local/bin/java
[01:26:47] Found snpEff - /usr/local/bin/snpEff
[01:26:47] Found samclip - /usr/local/bin/samclip
[01:26:47] Found seqtk - /usr/local/bin/seqtk
[01:26:47] Found parallel - /usr/local/bin/parallel
[01:26:47] Found freebayes - /usr/local/bin/freebayes
[01:26:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:26:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:26:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:26:47] Found vcfuniq - /usr/local/bin/vcfuniq
[01:26:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:26:47] Found gzip - /bin/gzip
[01:26:47] Found vt - /usr/local/bin/vt
[01:26:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:26:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:26:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:26:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:26:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:26:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:26:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:26:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:34:29] This is snippy 4.6.0Show full stderr[01:34:29] This is snippy 4.6.0
[01:34:29] Written by Torsten Seemann
[01:34:29] Obtained from https://github.com/tseemann/snippy
[01:34:29] Detected operating system: linux
[01:34:29] Enabling bundled linux tools.
[01:34:29] Found bwa - /usr/local/bin/bwa
[01:34:29] Found bcftools - /usr/local/bin/bcftools
[01:34:29] Found samtools - /usr/local/bin/samtools
[01:34:29] Found java - /usr/local/bin/java
[01:34:29] Found snpEff - /usr/local/bin/snpEff
[01:34:29] Found samclip - /usr/local/bin/samclip
[01:34:29] Found seqtk - /usr/local/bin/seqtk
[01:34:29] Found parallel - /usr/local/bin/parallel
[01:34:29] Found freebayes - /usr/local/bin/freebayes
[01:34:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:34:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:34:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:34:30] Found vcfuniq - /usr/local/bin/vcfuniq
[01:34:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:34:30] Found gzip - /bin/gzip
[01:34:30] Found vt - /usr/local/bin/vt
[01:34:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:34:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:34:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:34:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:34:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:34:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:34:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:34:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:34:41] This is snippy 4.6.0Show full stderr[01:34:41] This is snippy 4.6.0
[01:34:41] Written by Torsten Seemann
[01:34:41] Obtained from https://github.com/tseemann/snippy
[01:34:41] Detected operating system: linux
[01:34:41] Enabling bundled linux tools.
[01:34:41] Found bwa - /usr/local/bin/bwa
[01:34:41] Found bcftools - /usr/local/bin/bcftools
[01:34:41] Found samtools - /usr/local/bin/samtools
[01:34:41] Found java - /usr/local/bin/java
[01:34:41] Found snpEff - /usr/local/bin/snpEff
[01:34:41] Found samclip - /usr/local/bin/samclip
[01:34:41] Found seqtk - /usr/local/bin/seqtk
[01:34:41] Found parallel - /usr/local/bin/parallel
[01:34:41] Found freebayes - /usr/local/bin/freebayes
[01:34:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:34:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:34:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:34:41] Found vcfuniq - /usr/local/bin/vcfuniq
[01:34:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:34:41] Found gzip - /bin/gzip
[01:34:41] Found vt - /usr/local/bin/vt
[01:34:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:34:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:34:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:34:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:34:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:34:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:34:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:34:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:34:55] This is snippy 4.6.0Show full stderr[01:34:55] This is snippy 4.6.0
[01:34:55] Written by Torsten Seemann
[01:34:55] Obtained from https://github.com/tseemann/snippy
[01:34:55] Detected operating system: linux
[01:34:55] Enabling bundled linux tools.
[01:34:55] Found bwa - /usr/local/bin/bwa
[01:34:55] Found bcftools - /usr/local/bin/bcftools
[01:34:55] Found samtools - /usr/local/bin/samtools
[01:34:55] Found java - /usr/local/bin/java
[01:34:55] Found snpEff - /usr/local/bin/snpEff
[01:34:55] Found samclip - /usr/local/bin/samclip
[01:34:55] Found seqtk - /usr/local/bin/seqtk
[01:34:55] Found parallel - /usr/local/bin/parallel
[01:34:55] Found freebayes - /usr/local/bin/freebayes
[01:34:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:34:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:34:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:34:55] Found vcfuniq - /usr/local/bin/vcfuniq
[01:34:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:34:55] Found gzip - /bin/gzip
[01:34:55] Found vt - /usr/local/bin/vt
[01:34:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:34:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:34:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:34:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:34:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:34:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:34:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:34:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:43:17] This is snippy 4.6.0Show full stderr[01:43:17] This is snippy 4.6.0
[01:43:17] Written by Torsten Seemann
[01:43:17] Obtained from https://github.com/tseemann/snippy
[01:43:17] Detected operating system: linux
[01:43:17] Enabling bundled linux tools.
[01:43:17] Found bwa - /usr/local/bin/bwa
[01:43:17] Found bcftools - /usr/local/bin/bcftools
[01:43:17] Found samtools - /usr/local/bin/samtools
[01:43:17] Found java - /usr/local/bin/java
[01:43:17] Found snpEff - /usr/local/bin/snpEff
[01:43:17] Found samclip - /usr/local/bin/samclip
[01:43:17] Found seqtk - /usr/local/bin/seqtk
[01:43:17] Found parallel - /usr/local/bin/parallel
[01:43:17] Found freebayes - /usr/local/bin/freebayes
[01:43:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:43:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:43:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:43:17] Found vcfuniq - /usr/local/bin/vcfuniq
[01:43:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:43:17] Found gzip - /bin/gzip
[01:43:17] Found vt - /usr/local/bin/vt
[01:43:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:43:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:43:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:43:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:43:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:43:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:43:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:43:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:51:32] This is snippy 4.6.0Show full stderr[01:51:32] This is snippy 4.6.0
[01:51:32] Written by Torsten Seemann
[01:51:32] Obtained from https://github.com/tseemann/snippy
[01:51:32] Detected operating system: linux
[01:51:32] Enabling bundled linux tools.
[01:51:32] Found bwa - /usr/local/bin/bwa
[01:51:32] Found bcftools - /usr/local/bin/bcftools
[01:51:32] Found samtools - /usr/local/bin/samtools
[01:51:32] Found java - /usr/local/bin/java
[01:51:32] Found snpEff - /usr/local/bin/snpEff
[01:51:32] Found samclip - /usr/local/bin/samclip
[01:51:32] Found seqtk - /usr/local/bin/seqtk
[01:51:32] Found parallel - /usr/local/bin/parallel
[01:51:32] Found freebayes - /usr/local/bin/freebayes
[01:51:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:51:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:51:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:51:32] Found vcfuniq - /usr/local/bin/vcfuniq
[01:51:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:51:32] Found gzip - /bin/gzip
[01:51:32] Found vt - /usr/local/bin/vt
[01:51:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:51:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:51:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:51:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:51:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:51:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:51:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:51:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:52:17] This is snippy 4.6.0Show full stderr[01:52:17] This is snippy 4.6.0
[01:52:17] Written by Torsten Seemann
[01:52:17] Obtained from https://github.com/tseemann/snippy
[01:52:17] Detected operating system: linux
[01:52:17] Enabling bundled linux tools.
[01:52:17] Found bwa - /usr/local/bin/bwa
[01:52:17] Found bcftools - /usr/local/bin/bcftools
[01:52:17] Found samtools - /usr/local/bin/samtools
[01:52:17] Found java - /usr/local/bin/java
[01:52:17] Found snpEff - /usr/local/bin/snpEff
[01:52:17] Found samclip - /usr/local/bin/samclip
[01:52:17] Found seqtk - /usr/local/bin/seqtk
[01:52:17] Found parallel - /usr/local/bin/parallel
[01:52:17] Found freebayes - /usr/local/bin/freebayes
[01:52:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:52:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:52:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:52:17] Found vcfuniq - /usr/local/bin/vcfuniq
[01:52:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:52:17] Found gzip - /bin/gzip
[01:52:17] Found vt - /usr/local/bin/vt
[01:52:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:52:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:52:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:52:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:52:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:52:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:52:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:52:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:59:58] This is snippy 4.6.0Show full stderr[01:59:58] This is snippy 4.6.0
[01:59:58] Written by Torsten Seemann
[01:59:58] Obtained from https://github.com/tseemann/snippy
[01:59:58] Detected operating system: linux
[01:59:58] Enabling bundled linux tools.
[01:59:58] Found bwa - /usr/local/bin/bwa
[01:59:58] Found bcftools - /usr/local/bin/bcftools
[01:59:58] Found samtools - /usr/local/bin/samtools
[01:59:58] Found java - /usr/local/bin/java
[01:59:58] Found snpEff - /usr/local/bin/snpEff
[01:59:58] Found samclip - /usr/local/bin/samclip
[01:59:58] Found seqtk - /usr/local/bin/seqtk
[01:59:58] Found parallel - /usr/local/bin/parallel
[01:59:58] Found freebayes - /usr/local/bin/freebayes
[01:59:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:59:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:59:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:59:58] Found vcfuniq - /usr/local/bin/vcfuniq
[01:59:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:59:58] Found gzip - /bin/gzip
[01:59:58] Found vt - /usr/local/bin/vt
[01:59:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:59:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:59:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:59:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:59:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:59:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:59:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:59:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:20:17] This is snippy 4.6.0Show full stderr[22:20:17] This is snippy 4.6.0
[22:20:17] Written by Torsten Seemann
[22:20:17] Obtained from https://github.com/tseemann/snippy
[22:20:17] Detected operating system: linux
[22:20:17] Enabling bundled linux tools.
[22:20:17] Found bwa - /usr/local/bin/bwa
[22:20:17] Found bcftools - /usr/local/bin/bcftools
[22:20:17] Found samtools - /usr/local/bin/samtools
[22:20:17] Found java - /usr/local/bin/java
[22:20:17] Found snpEff - /usr/local/bin/snpEff
[22:20:17] Found samclip - /usr/local/bin/samclip
[22:20:17] Found seqtk - /usr/local/bin/seqtk
[22:20:17] Found parallel - /usr/local/bin/parallel
[22:20:17] Found freebayes - /usr/local/bin/freebayes
[22:20:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:20:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:20:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:20:17] Found vcfuniq - /usr/local/bin/vcfuniq
[22:20:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:20:18] Found gzip - /bin/gzip
[22:20:18] Found vt - /usr/local/bin/vt
[22:20:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:20:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:20:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:20:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:20:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:20:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:20:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:20:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:29:17] This is snippy 4.6.0Show full stderr[22:29:17] This is snippy 4.6.0
[22:29:17] Written by Torsten Seemann
[22:29:17] Obtained from https://github.com/tseemann/snippy
[22:29:17] Detected operating system: linux
[22:29:17] Enabling bundled linux tools.
[22:29:17] Found bwa - /usr/local/bin/bwa
[22:29:17] Found bcftools - /usr/local/bin/bcftools
[22:29:17] Found samtools - /usr/local/bin/samtools
[22:29:17] Found java - /usr/local/bin/java
[22:29:17] Found snpEff - /usr/local/bin/snpEff
[22:29:17] Found samclip - /usr/local/bin/samclip
[22:29:18] Found seqtk - /usr/local/bin/seqtk
[22:29:18] Found parallel - /usr/local/bin/parallel
[22:29:18] Found freebayes - /usr/local/bin/freebayes
[22:29:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:29:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:29:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:29:18] Found vcfuniq - /usr/local/bin/vcfuniq
[22:29:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:29:18] Found gzip - /bin/gzip
[22:29:18] Found vt - /usr/local/bin/vt
[22:29:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:29:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:29:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:29:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:29:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:29:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:29:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:29:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:01:52] This is snippy 4.6.0Show full stderr[23:01:52] This is snippy 4.6.0
[23:01:52] Written by Torsten Seemann
[23:01:52] Obtained from https://github.com/tseemann/snippy
[23:01:52] Detected operating system: linux
[23:01:52] Enabling bundled linux tools.
[23:01:52] Found bwa - /usr/local/bin/bwa
[23:01:52] Found bcftools - /usr/local/bin/bcftools
[23:01:52] Found samtools - /usr/local/bin/samtools
[23:01:52] Found java - /usr/local/bin/java
[23:01:52] Found snpEff - /usr/local/bin/snpEff
[23:01:52] Found samclip - /usr/local/bin/samclip
[23:01:52] Found seqtk - /usr/local/bin/seqtk
[23:01:52] Found parallel - /usr/local/bin/parallel
[23:01:52] Found freebayes - /usr/local/bin/freebayes
[23:01:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:01:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:01:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:01:52] Found vcfuniq - /usr/local/bin/vcfuniq
[23:01:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:01:52] Found gzip - /bin/gzip
[23:01:52] Found vt - /usr/local/bin/vt
[23:01:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:01:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:01:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:01:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:01:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:01:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:01:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:01:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:10:00] This is snippy 4.6.0Show full stderr[23:10:00] This is snippy 4.6.0
[23:10:00] Written by Torsten Seemann
[23:10:00] Obtained from https://github.com/tseemann/snippy
[23:10:00] Detected operating system: linux
[23:10:00] Enabling bundled linux tools.
[23:10:00] Found bwa - /usr/local/bin/bwa
[23:10:00] Found bcftools - /usr/local/bin/bcftools
[23:10:00] Found samtools - /usr/local/bin/samtools
[23:10:00] Found java - /usr/local/bin/java
[23:10:00] Found snpEff - /usr/local/bin/snpEff
[23:10:00] Found samclip - /usr/local/bin/samclip
[23:10:00] Found seqtk - /usr/local/bin/seqtk
[23:10:00] Found parallel - /usr/local/bin/parallel
[23:10:00] Found freebayes - /usr/local/bin/freebayes
[23:10:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:10:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:10:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:10:00] Found vcfuniq - /usr/local/bin/vcfuniq
[23:10:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:10:00] Found gzip - /bin/gzip
[23:10:00] Found vt - /usr/local/bin/vt
[23:10:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:10:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:10:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:10:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:10:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:10:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:10:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:10:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:10:48] This is snippy 4.6.0Show full stderr[23:10:48] This is snippy 4.6.0
[23:10:48] Written by Torsten Seemann
[23:10:48] Obtained from https://github.com/tseemann/snippy
[23:10:48] Detected operating system: linux
[23:10:48] Enabling bundled linux tools.
[23:10:48] Found bwa - /usr/local/bin/bwa
[23:10:48] Found bcftools - /usr/local/bin/bcftools
[23:10:48] Found samtools - /usr/local/bin/samtools
[23:10:48] Found java - /usr/local/bin/java
[23:10:48] Found snpEff - /usr/local/bin/snpEff
[23:10:48] Found samclip - /usr/local/bin/samclip
[23:10:48] Found seqtk - /usr/local/bin/seqtk
[23:10:48] Found parallel - /usr/local/bin/parallel
[23:10:48] Found freebayes - /usr/local/bin/freebayes
[23:10:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:10:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:10:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:10:48] Found vcfuniq - /usr/local/bin/vcfuniq
[23:10:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:10:48] Found gzip - /bin/gzip
[23:10:48] Found vt - /usr/local/bin/vt
[23:10:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:10:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:10:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:10:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:10:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:10:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:10:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:10:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:18:27] This is snippy 4.6.0Show full stderr[23:18:27] This is snippy 4.6.0
[23:18:27] Written by Torsten Seemann
[23:18:27] Obtained from https://github.com/tseemann/snippy
[23:18:27] Detected operating system: linux
[23:18:27] Enabling bundled linux tools.
[23:18:27] Found bwa - /usr/local/bin/bwa
[23:18:27] Found bcftools - /usr/local/bin/bcftools
[23:18:27] Found samtools - /usr/local/bin/samtools
[23:18:27] Found java - /usr/local/bin/java
[23:18:27] Found snpEff - /usr/local/bin/snpEff
[23:18:27] Found samclip - /usr/local/bin/samclip
[23:18:27] Found seqtk - /usr/local/bin/seqtk
[23:18:27] Found parallel - /usr/local/bin/parallel
[23:18:27] Found freebayes - /usr/local/bin/freebayes
[23:18:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:18:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:18:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:18:27] Found vcfuniq - /usr/local/bin/vcfuniq
[23:18:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:18:27] Found gzip - /bin/gzip
[23:18:27] Found vt - /usr/local/bin/vt
[23:18:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:18:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:18:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:18:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:18:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:18:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:18:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:18:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:58:57] This is snippy 4.6.0Show full stderr[23:58:57] This is snippy 4.6.0
[23:58:57] Written by Torsten Seemann
[23:58:57] Obtained from https://github.com/tseemann/snippy
[23:58:57] Detected operating system: linux
[23:58:57] Enabling bundled linux tools.
[23:58:57] Found bwa - /usr/local/bin/bwa
[23:58:57] Found bcftools - /usr/local/bin/bcftools
[23:58:57] Found samtools - /usr/local/bin/samtools
[23:58:57] Found java - /usr/local/bin/java
[23:58:57] Found snpEff - /usr/local/bin/snpEff
[23:58:57] Found samclip - /usr/local/bin/samclip
[23:58:57] Found seqtk - /usr/local/bin/seqtk
[23:58:57] Found parallel - /usr/local/bin/parallel
[23:58:57] Found freebayes - /usr/local/bin/freebayes
[23:58:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:58:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:58:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:58:57] Found vcfuniq - /usr/local/bin/vcfuniq
[23:58:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:58:57] Found gzip - /bin/gzip
[23:58:57] Found vt - /usr/local/bin/vt
[23:58:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:58:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:58:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:58:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:58:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:58:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:58:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:58:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:25:08] This is snippy 4.6.0Show full stderr[00:25:08] This is snippy 4.6.0
[00:25:08] Written by Torsten Seemann
[00:25:08] Obtained from https://github.com/tseemann/snippy
[00:25:08] Detected operating system: linux
[00:25:08] Enabling bundled linux tools.
[00:25:08] Found bwa - /usr/local/bin/bwa
[00:25:08] Found bcftools - /usr/local/bin/bcftools
[00:25:08] Found samtools - /usr/local/bin/samtools
[00:25:08] Found java - /usr/local/bin/java
[00:25:08] Found snpEff - /usr/local/bin/snpEff
[00:25:08] Found samclip - /usr/local/bin/samclip
[00:25:08] Found seqtk - /usr/local/bin/seqtk
[00:25:08] Found parallel - /usr/local/bin/parallel
[00:25:08] Found freebayes - /usr/local/bin/freebayes
[00:25:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:25:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:25:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:25:08] Found vcfuniq - /usr/local/bin/vcfuniq
[00:25:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:25:08] Found gzip - /bin/gzip
[00:25:08] Found vt - /usr/local/bin/vt
[00:25:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:25:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:25:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:25:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:25:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:25:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:25:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:25:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:08:11] This is snippy 4.6.0Show full stderr[00:08:11] This is snippy 4.6.0
[00:08:11] Written by Torsten Seemann
[00:08:11] Obtained from https://github.com/tseemann/snippy
[00:08:11] Detected operating system: linux
[00:08:11] Enabling bundled linux tools.
[00:08:11] Found bwa - /usr/local/bin/bwa
[00:08:12] Found bcftools - /usr/local/bin/bcftools
[00:08:12] Found samtools - /usr/local/bin/samtools
[00:08:12] Found java - /usr/local/bin/java
[00:08:12] Found snpEff - /usr/local/bin/snpEff
[00:08:12] Found samclip - /usr/local/bin/samclip
[00:08:12] Found seqtk - /usr/local/bin/seqtk
[00:08:12] Found parallel - /usr/local/bin/parallel
[00:08:12] Found freebayes - /usr/local/bin/freebayes
[00:08:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:08:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:08:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:08:12] Found vcfuniq - /usr/local/bin/vcfuniq
[00:08:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:08:12] Found gzip - /bin/gzip
[00:08:12] Found vt - /usr/local/bin/vt
[00:08:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:08:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:08:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:08:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:08:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:08:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:08:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:08:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:33:06] This is snippy 4.6.0Show full stderr[00:33:06] This is snippy 4.6.0
[00:33:06] Written by Torsten Seemann
[00:33:06] Obtained from https://github.com/tseemann/snippy
[00:33:06] Detected operating system: linux
[00:33:06] Enabling bundled linux tools.
[00:33:06] Found bwa - /usr/local/bin/bwa
[00:33:06] Found bcftools - /usr/local/bin/bcftools
[00:33:06] Found samtools - /usr/local/bin/samtools
[00:33:06] Found java - /usr/local/bin/java
[00:33:06] Found snpEff - /usr/local/bin/snpEff
[00:33:06] Found samclip - /usr/local/bin/samclip
[00:33:06] Found seqtk - /usr/local/bin/seqtk
[00:33:06] Found parallel - /usr/local/bin/parallel
[00:33:06] Found freebayes - /usr/local/bin/freebayes
[00:33:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:06] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:06] Found gzip - /bin/gzip
[00:33:06] Found vt - /usr/local/bin/vt
[00:33:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:43:10] This is snippy 4.6.0Show full stderr[00:43:10] This is snippy 4.6.0
[00:43:10] Written by Torsten Seemann
[00:43:10] Obtained from https://github.com/tseemann/snippy
[00:43:10] Detected operating system: linux
[00:43:10] Enabling bundled linux tools.
[00:43:10] Found bwa - /usr/local/bin/bwa
[00:43:10] Found bcftools - /usr/local/bin/bcftools
[00:43:10] Found samtools - /usr/local/bin/samtools
[00:43:10] Found java - /usr/local/bin/java
[00:43:10] Found snpEff - /usr/local/bin/snpEff
[00:43:10] Found samclip - /usr/local/bin/samclip
[00:43:10] Found seqtk - /usr/local/bin/seqtk
[00:43:10] Found parallel - /usr/local/bin/parallel
[00:43:10] Found freebayes - /usr/local/bin/freebayes
[00:43:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:43:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:43:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:43:10] Found vcfuniq - /usr/local/bin/vcfuniq
[00:43:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:43:10] Found gzip - /bin/gzip
[00:43:10] Found vt - /usr/local/bin/vt
[00:43:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:43:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:43:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:43:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:43:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:43:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:43:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:43:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:14:48] This is snippy 4.6.0Show full stderr[20:14:48] This is snippy 4.6.0
[20:14:48] Written by Torsten Seemann
[20:14:48] Obtained from https://github.com/tseemann/snippy
[20:14:48] Detected operating system: linux
[20:14:48] Enabling bundled linux tools.
[20:14:48] Found bwa - /usr/local/bin/bwa
[20:14:48] Found bcftools - /usr/local/bin/bcftools
[20:14:48] Found samtools - /usr/local/bin/samtools
[20:14:48] Found java - /usr/local/bin/java
[20:14:48] Found snpEff - /usr/local/bin/snpEff
[20:14:48] Found samclip - /usr/local/bin/samclip
[20:14:48] Found seqtk - /usr/local/bin/seqtk
[20:14:48] Found parallel - /usr/local/bin/parallel
[20:14:48] Found freebayes - /usr/local/bin/freebayes
[20:14:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:14:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:14:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:14:48] Found vcfuniq - /usr/local/bin/vcfuniq
[20:14:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:14:48] Found gzip - /bin/gzip
[20:14:48] Found vt - /usr/local/bin/vt
[20:14:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:14:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:14:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:14:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:14:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:14:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:14:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:14:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:44:48] This is snippy 4.6.0Show full stderr[00:44:48] This is snippy 4.6.0
[00:44:48] Written by Torsten Seemann
[00:44:48] Obtained from https://github.com/tseemann/snippy
[00:44:48] Detected operating system: linux
[00:44:48] Enabling bundled linux tools.
[00:44:48] Found bwa - /usr/local/bin/bwa
[00:44:48] Found bcftools - /usr/local/bin/bcftools
[00:44:48] Found samtools - /usr/local/bin/samtools
[00:44:48] Found java - /usr/local/bin/java
[00:44:48] Found snpEff - /usr/local/bin/snpEff
[00:44:48] Found samclip - /usr/local/bin/samclip
[00:44:48] Found seqtk - /usr/local/bin/seqtk
[00:44:48] Found parallel - /usr/local/bin/parallel
[00:44:48] Found freebayes - /usr/local/bin/freebayes
[00:44:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:44:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:44:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:44:48] Found vcfuniq - /usr/local/bin/vcfuniq
[00:44:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:44:48] Found gzip - /bin/gzip
[00:44:48] Found vt - /usr/local/bin/vt
[00:44:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:44:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:44:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:44:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:44:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:44:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:44:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:44:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:53:18] This is snippy 4.6.0Show full stderr[00:53:18] This is snippy 4.6.0
[00:53:18] Written by Torsten Seemann
[00:53:18] Obtained from https://github.com/tseemann/snippy
[00:53:18] Detected operating system: linux
[00:53:18] Enabling bundled linux tools.
[00:53:18] Found bwa - /usr/local/bin/bwa
[00:53:18] Found bcftools - /usr/local/bin/bcftools
[00:53:18] Found samtools - /usr/local/bin/samtools
[00:53:18] Found java - /usr/local/bin/java
[00:53:18] Found snpEff - /usr/local/bin/snpEff
[00:53:18] Found samclip - /usr/local/bin/samclip
[00:53:18] Found seqtk - /usr/local/bin/seqtk
[00:53:18] Found parallel - /usr/local/bin/parallel
[00:53:18] Found freebayes - /usr/local/bin/freebayes
[00:53:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:53:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:53:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:53:18] Found vcfuniq - /usr/local/bin/vcfuniq
[00:53:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:53:18] Found gzip - /bin/gzip
[00:53:18] Found vt - /usr/local/bin/vt
[00:53:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:53:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:53:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:53:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:53:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:53:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:53:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:53:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:49:48] This is snippy 4.6.0Show full stderr[19:49:48] This is snippy 4.6.0
[19:49:48] Written by Torsten Seemann
[19:49:48] Obtained from https://github.com/tseemann/snippy
[19:49:48] Detected operating system: linux
[19:49:48] Enabling bundled linux tools.
[19:49:48] Found bwa - /usr/local/bin/bwa
[19:49:48] Found bcftools - /usr/local/bin/bcftools
[19:49:48] Found samtools - /usr/local/bin/samtools
[19:49:48] Found java - /usr/local/bin/java
[19:49:48] Found snpEff - /usr/local/bin/snpEff
[19:49:48] Found samclip - /usr/local/bin/samclip
[19:49:48] Found seqtk - /usr/local/bin/seqtk
[19:49:48] Found parallel - /usr/local/bin/parallel
[19:49:48] Found freebayes - /usr/local/bin/freebayes
[19:49:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:49:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:49:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:49:48] Found vcfuniq - /usr/local/bin/vcfuniq
[19:49:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:49:48] Found gzip - /bin/gzip
[19:49:48] Found vt - /usr/local/bin/vt
[19:49:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:49:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:49:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:49:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:49:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:49:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:49:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:49:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:57:48] This is snippy 4.6.0Show full stderr[19:57:48] This is snippy 4.6.0
[19:57:48] Written by Torsten Seemann
[19:57:48] Obtained from https://github.com/tseemann/snippy
[19:57:48] Detected operating system: linux
[19:57:48] Enabling bundled linux tools.
[19:57:48] Found bwa - /usr/local/bin/bwa
[19:57:48] Found bcftools - /usr/local/bin/bcftools
[19:57:48] Found samtools - /usr/local/bin/samtools
[19:57:48] Found java - /usr/local/bin/java
[19:57:48] Found snpEff - /usr/local/bin/snpEff
[19:57:48] Found samclip - /usr/local/bin/samclip
[19:57:48] Found seqtk - /usr/local/bin/seqtk
[19:57:48] Found parallel - /usr/local/bin/parallel
[19:57:48] Found freebayes - /usr/local/bin/freebayes
[19:57:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:57:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:57:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:57:48] Found vcfuniq - /usr/local/bin/vcfuniq
[19:57:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:57:48] Found gzip - /bin/gzip
[19:57:48] Found vt - /usr/local/bin/vt
[19:57:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:57:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:57:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:57:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:57:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:57:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:57:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:57:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:18:47] This is snippy 4.6.0Show full stderr[18:18:47] This is snippy 4.6.0
[18:18:47] Written by Torsten Seemann
[18:18:47] Obtained from https://github.com/tseemann/snippy
[18:18:47] Detected operating system: linux
[18:18:47] Enabling bundled linux tools.
[18:18:47] Found bwa - /usr/local/bin/bwa
[18:18:47] Found bcftools - /usr/local/bin/bcftools
[18:18:47] Found samtools - /usr/local/bin/samtools
[18:18:47] Found java - /usr/local/bin/java
[18:18:47] Found snpEff - /usr/local/bin/snpEff
[18:18:47] Found samclip - /usr/local/bin/samclip
[18:18:47] Found seqtk - /usr/local/bin/seqtk
[18:18:47] Found parallel - /usr/local/bin/parallel
[18:18:47] Found freebayes - /usr/local/bin/freebayes
[18:18:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:18:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:18:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:18:48] Found vcfuniq - /usr/local/bin/vcfuniq
[18:18:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:18:48] Found gzip - /bin/gzip
[18:18:48] Found vt - /usr/local/bin/vt
[18:18:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:18:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:18:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:18:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:18:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:18:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:18:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:18:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:38:31] This is snippy 4.6.0Show full stderr[20:38:31] This is snippy 4.6.0
[20:38:31] Written by Torsten Seemann
[20:38:31] Obtained from https://github.com/tseemann/snippy
[20:38:31] Detected operating system: linux
[20:38:31] Enabling bundled linux tools.
[20:38:31] Found bwa - /usr/local/bin/bwa
[20:38:31] Found bcftools - /usr/local/bin/bcftools
[20:38:31] Found samtools - /usr/local/bin/samtools
[20:38:31] Found java - /usr/local/bin/java
[20:38:31] Found snpEff - /usr/local/bin/snpEff
[20:38:31] Found samclip - /usr/local/bin/samclip
[20:38:31] Found seqtk - /usr/local/bin/seqtk
[20:38:31] Found parallel - /usr/local/bin/parallel
[20:38:31] Found freebayes - /usr/local/bin/freebayes
[20:38:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:38:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:38:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:38:31] Found vcfuniq - /usr/local/bin/vcfuniq
[20:38:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:38:31] Found gzip - /bin/gzip
[20:38:31] Found vt - /usr/local/bin/vt
[20:38:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:38:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:38:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:38:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:38:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:38:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:38:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:38:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:45:17] This is snippy 4.6.0Show full stderr[17:45:17] This is snippy 4.6.0
[17:45:17] Written by Torsten Seemann
[17:45:17] Obtained from https://github.com/tseemann/snippy
[17:45:17] Detected operating system: linux
[17:45:17] Enabling bundled linux tools.
[17:45:17] Found bwa - /usr/local/bin/bwa
[17:45:17] Found bcftools - /usr/local/bin/bcftools
[17:45:17] Found samtools - /usr/local/bin/samtools
[17:45:17] Found java - /usr/local/bin/java
[17:45:17] Found snpEff - /usr/local/bin/snpEff
[17:45:17] Found samclip - /usr/local/bin/samclip
[17:45:17] Found seqtk - /usr/local/bin/seqtk
[17:45:17] Found parallel - /usr/local/bin/parallel
[17:45:17] Found freebayes - /usr/local/bin/freebayes
[17:45:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:45:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:45:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:45:17] Found vcfuniq - /usr/local/bin/vcfuniq
[17:45:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:45:17] Found gzip - /bin/gzip
[17:45:17] Found vt - /usr/local/bin/vt
[17:45:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:45:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:45:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:45:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:45:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:38:54] This is snippy 4.6.0Show full stderr[20:38:54] This is snippy 4.6.0
[20:38:54] Written by Torsten Seemann
[20:38:54] Obtained from https://github.com/tseemann/snippy
[20:38:54] Detected operating system: linux
[20:38:54] Enabling bundled linux tools.
[20:38:54] Found bwa - /usr/local/bin/bwa
[20:38:54] Found bcftools - /usr/local/bin/bcftools
[20:38:54] Found samtools - /usr/local/bin/samtools
[20:38:54] Found java - /usr/local/bin/java
[20:38:54] Found snpEff - /usr/local/bin/snpEff
[20:38:54] Found samclip - /usr/local/bin/samclip
[20:38:54] Found seqtk - /usr/local/bin/seqtk
[20:38:54] Found parallel - /usr/local/bin/parallel
[20:38:54] Found freebayes - /usr/local/bin/freebayes
[20:38:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:38:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:38:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:38:54] Found vcfuniq - /usr/local/bin/vcfuniq
[20:38:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:38:54] Found gzip - /bin/gzip
[20:38:54] Found vt - /usr/local/bin/vt
[20:38:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:38:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:38:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:38:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:38:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:38:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:38:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:38:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:03:39] This is snippy 4.6.0Show full stderr[21:03:39] This is snippy 4.6.0
[21:03:39] Written by Torsten Seemann
[21:03:39] Obtained from https://github.com/tseemann/snippy
[21:03:39] Detected operating system: linux
[21:03:39] Enabling bundled linux tools.
[21:03:39] Found bwa - /usr/local/bin/bwa
[21:03:39] Found bcftools - /usr/local/bin/bcftools
[21:03:39] Found samtools - /usr/local/bin/samtools
[21:03:39] Found java - /usr/local/bin/java
[21:03:39] Found snpEff - /usr/local/bin/snpEff
[21:03:39] Found samclip - /usr/local/bin/samclip
[21:03:39] Found seqtk - /usr/local/bin/seqtk
[21:03:39] Found parallel - /usr/local/bin/parallel
[21:03:39] Found freebayes - /usr/local/bin/freebayes
[21:03:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:03:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:03:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:03:39] Found vcfuniq - /usr/local/bin/vcfuniq
[21:03:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:03:39] Found gzip - /bin/gzip
[21:03:39] Found vt - /usr/local/bin/vt
[21:03:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:03:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:03:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:03:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:03:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:03:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:03:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:03:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:30:47] This is snippy 4.6.0Show full stderr[21:30:47] This is snippy 4.6.0
[21:30:47] Written by Torsten Seemann
[21:30:47] Obtained from https://github.com/tseemann/snippy
[21:30:47] Detected operating system: linux
[21:30:47] Enabling bundled linux tools.
[21:30:47] Found bwa - /usr/local/bin/bwa
[21:30:47] Found bcftools - /usr/local/bin/bcftools
[21:30:47] Found samtools - /usr/local/bin/samtools
[21:30:47] Found java - /usr/local/bin/java
[21:30:47] Found snpEff - /usr/local/bin/snpEff
[21:30:47] Found samclip - /usr/local/bin/samclip
[21:30:47] Found seqtk - /usr/local/bin/seqtk
[21:30:47] Found parallel - /usr/local/bin/parallel
[21:30:47] Found freebayes - /usr/local/bin/freebayes
[21:30:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:30:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:30:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:30:47] Found vcfuniq - /usr/local/bin/vcfuniq
[21:30:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:30:47] Found gzip - /bin/gzip
[21:30:47] Found vt - /usr/local/bin/vt
[21:30:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:30:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:30:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:30:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:30:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:30:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:30:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:30:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:55:17] This is snippy 4.6.0Show full stderr[21:55:17] This is snippy 4.6.0
[21:55:17] Written by Torsten Seemann
[21:55:17] Obtained from https://github.com/tseemann/snippy
[21:55:17] Detected operating system: linux
[21:55:17] Enabling bundled linux tools.
[21:55:17] Found bwa - /usr/local/bin/bwa
[21:55:17] Found bcftools - /usr/local/bin/bcftools
[21:55:17] Found samtools - /usr/local/bin/samtools
[21:55:17] Found java - /usr/local/bin/java
[21:55:17] Found snpEff - /usr/local/bin/snpEff
[21:55:17] Found samclip - /usr/local/bin/samclip
[21:55:17] Found seqtk - /usr/local/bin/seqtk
[21:55:17] Found parallel - /usr/local/bin/parallel
[21:55:17] Found freebayes - /usr/local/bin/freebayes
[21:55:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:55:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:55:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:55:17] Found vcfuniq - /usr/local/bin/vcfuniq
[21:55:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:55:17] Found gzip - /bin/gzip
[21:55:17] Found vt - /usr/local/bin/vt
[21:55:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:55:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:55:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:55:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:55:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:55:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:55:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:55:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:03:04] This is snippy 4.6.0Show full stderr[22:03:04] This is snippy 4.6.0
[22:03:04] Written by Torsten Seemann
[22:03:04] Obtained from https://github.com/tseemann/snippy
[22:03:04] Detected operating system: linux
[22:03:04] Enabling bundled linux tools.
[22:03:04] Found bwa - /usr/local/bin/bwa
[22:03:04] Found bcftools - /usr/local/bin/bcftools
[22:03:04] Found samtools - /usr/local/bin/samtools
[22:03:04] Found java - /usr/local/bin/java
[22:03:04] Found snpEff - /usr/local/bin/snpEff
[22:03:04] Found samclip - /usr/local/bin/samclip
[22:03:04] Found seqtk - /usr/local/bin/seqtk
[22:03:04] Found parallel - /usr/local/bin/parallel
[22:03:04] Found freebayes - /usr/local/bin/freebayes
[22:03:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:03:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:03:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:03:04] Found vcfuniq - /usr/local/bin/vcfuniq
[22:03:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:03:04] Found gzip - /bin/gzip
[22:03:04] Found vt - /usr/local/bin/vt
[22:03:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:03:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:03:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:03:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:03:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:03:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:03:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:03:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:11:47] This is snippy 4.6.0Show full stderr[22:11:47] This is snippy 4.6.0
[22:11:47] Written by Torsten Seemann
[22:11:47] Obtained from https://github.com/tseemann/snippy
[22:11:47] Detected operating system: linux
[22:11:47] Enabling bundled linux tools.
[22:11:47] Found bwa - /usr/local/bin/bwa
[22:11:47] Found bcftools - /usr/local/bin/bcftools
[22:11:47] Found samtools - /usr/local/bin/samtools
[22:11:47] Found java - /usr/local/bin/java
[22:11:47] Found snpEff - /usr/local/bin/snpEff
[22:11:47] Found samclip - /usr/local/bin/samclip
[22:11:47] Found seqtk - /usr/local/bin/seqtk
[22:11:47] Found parallel - /usr/local/bin/parallel
[22:11:47] Found freebayes - /usr/local/bin/freebayes
[22:11:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:11:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:11:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:11:47] Found vcfuniq - /usr/local/bin/vcfuniq
[22:11:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:11:47] Found gzip - /bin/gzip
[22:11:47] Found vt - /usr/local/bin/vt
[22:11:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:11:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:11:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:11:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:11:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:11:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:11:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:11:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:19:30] This is snippy 4.6.0Show full stderr[22:19:30] This is snippy 4.6.0
[22:19:30] Written by Torsten Seemann
[22:19:30] Obtained from https://github.com/tseemann/snippy
[22:19:30] Detected operating system: linux
[22:19:30] Enabling bundled linux tools.
[22:19:30] Found bwa - /usr/local/bin/bwa
[22:19:30] Found bcftools - /usr/local/bin/bcftools
[22:19:30] Found samtools - /usr/local/bin/samtools
[22:19:30] Found java - /usr/local/bin/java
[22:19:30] Found snpEff - /usr/local/bin/snpEff
[22:19:30] Found samclip - /usr/local/bin/samclip
[22:19:30] Found seqtk - /usr/local/bin/seqtk
[22:19:30] Found parallel - /usr/local/bin/parallel
[22:19:30] Found freebayes - /usr/local/bin/freebayes
[22:19:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:19:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:19:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:19:31] Found vcfuniq - /usr/local/bin/vcfuniq
[22:19:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:19:31] Found gzip - /bin/gzip
[22:19:31] Found vt - /usr/local/bin/vt
[22:19:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:19:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:19:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:19:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:19:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:19:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:19:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:19:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:37:17] This is snippy 4.6.0Show full stderr[22:37:17] This is snippy 4.6.0
[22:37:17] Written by Torsten Seemann
[22:37:17] Obtained from https://github.com/tseemann/snippy
[22:37:17] Detected operating system: linux
[22:37:17] Enabling bundled linux tools.
[22:37:17] Found bwa - /usr/local/bin/bwa
[22:37:17] Found bcftools - /usr/local/bin/bcftools
[22:37:17] Found samtools - /usr/local/bin/samtools
[22:37:17] Found java - /usr/local/bin/java
[22:37:17] Found snpEff - /usr/local/bin/snpEff
[22:37:17] Found samclip - /usr/local/bin/samclip
[22:37:17] Found seqtk - /usr/local/bin/seqtk
[22:37:17] Found parallel - /usr/local/bin/parallel
[22:37:17] Found freebayes - /usr/local/bin/freebayes
[22:37:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:37:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:37:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:37:17] Found vcfuniq - /usr/local/bin/vcfuniq
[22:37:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:37:18] Found gzip - /bin/gzip
[22:37:18] Found vt - /usr/local/bin/vt
[22:37:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:37:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:37:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:37:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:37:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:37:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:37:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:37:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:54:58] This is snippy 4.6.0Show full stderr[20:54:58] This is snippy 4.6.0
[20:54:58] Written by Torsten Seemann
[20:54:58] Obtained from https://github.com/tseemann/snippy
[20:54:58] Detected operating system: linux
[20:54:58] Enabling bundled linux tools.
[20:54:58] Found bwa - /usr/local/bin/bwa
[20:54:58] Found bcftools - /usr/local/bin/bcftools
[20:54:58] Found samtools - /usr/local/bin/samtools
[20:54:58] Found java - /usr/local/bin/java
[20:54:58] Found snpEff - /usr/local/bin/snpEff
[20:54:58] Found samclip - /usr/local/bin/samclip
[20:54:58] Found seqtk - /usr/local/bin/seqtk
[20:54:58] Found parallel - /usr/local/bin/parallel
[20:54:58] Found freebayes - /usr/local/bin/freebayes
[20:54:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:54:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:54:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:54:58] Found vcfuniq - /usr/local/bin/vcfuniq
[20:54:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:54:58] Found gzip - /bin/gzip
[20:54:58] Found vt - /usr/local/bin/vt
[20:54:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:54:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:54:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:54:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:54:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:54:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:54:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:54:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:55:48] This is snippy 4.6.0Show full stderr[20:55:48] This is snippy 4.6.0
[20:55:48] Written by Torsten Seemann
[20:55:48] Obtained from https://github.com/tseemann/snippy
[20:55:48] Detected operating system: linux
[20:55:48] Enabling bundled linux tools.
[20:55:48] Found bwa - /usr/local/bin/bwa
[20:55:48] Found bcftools - /usr/local/bin/bcftools
[20:55:48] Found samtools - /usr/local/bin/samtools
[20:55:48] Found java - /usr/local/bin/java
[20:55:48] Found snpEff - /usr/local/bin/snpEff
[20:55:48] Found samclip - /usr/local/bin/samclip
[20:55:48] Found seqtk - /usr/local/bin/seqtk
[20:55:48] Found parallel - /usr/local/bin/parallel
[20:55:48] Found freebayes - /usr/local/bin/freebayes
[20:55:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:55:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:55:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:55:48] Found vcfuniq - /usr/local/bin/vcfuniq
[20:55:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:55:48] Found gzip - /bin/gzip
[20:55:48] Found vt - /usr/local/bin/vt
[20:55:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:55:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:55:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:55:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:55:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:55:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:55:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:55:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:19:59] This is snippy 4.6.0Show full stderr[21:19:59] This is snippy 4.6.0
[21:19:59] Written by Torsten Seemann
[21:19:59] Obtained from https://github.com/tseemann/snippy
[21:19:59] Detected operating system: linux
[21:19:59] Enabling bundled linux tools.
[21:19:59] Found bwa - /usr/local/bin/bwa
[21:19:59] Found bcftools - /usr/local/bin/bcftools
[21:19:59] Found samtools - /usr/local/bin/samtools
[21:19:59] Found java - /usr/local/bin/java
[21:19:59] Found snpEff - /usr/local/bin/snpEff
[21:19:59] Found samclip - /usr/local/bin/samclip
[21:19:59] Found seqtk - /usr/local/bin/seqtk
[21:19:59] Found parallel - /usr/local/bin/parallel
[21:19:59] Found freebayes - /usr/local/bin/freebayes
[21:19:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:19:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:19:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:19:59] Found vcfuniq - /usr/local/bin/vcfuniq
[21:19:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:19:59] Found gzip - /bin/gzip
[21:19:59] Found vt - /usr/local/bin/vt
[21:19:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:19:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:19:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:19:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:19:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:20:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:20:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:20:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [19:24:00] This is snippy 4.6.0Show full stderr[19:24:00] This is snippy 4.6.0
[19:24:00] Written by Torsten Seemann
[19:24:00] Obtained from https://github.com/tseemann/snippy
[19:24:00] Detected operating system: linux
[19:24:00] Enabling bundled linux tools.
[19:24:00] Found bwa - /usr/local/bin/bwa
[19:24:00] Found bcftools - /usr/local/bin/bcftools
[19:24:00] Found samtools - /usr/local/bin/samtools
[19:24:00] Found java - /usr/local/bin/java
[19:24:00] Found snpEff - /usr/local/bin/snpEff
[19:24:00] Found samclip - /usr/local/bin/samclip
[19:24:00] Found seqtk - /usr/local/bin/seqtk
[19:24:00] Found parallel - /usr/local/bin/parallel
[19:24:00] Found freebayes - /usr/local/bin/freebayes
[19:24:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:24:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:24:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:24:00] Found vcfuniq - /usr/local/bin/vcfuniq
[19:24:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:24:00] Found gzip - /bin/gzip
[19:24:00] Found vt - /usr/local/bin/vt
[19:24:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:24:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:24:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:24:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:24:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:24:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:24:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:24:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:21:22] This is snippy 4.6.0Show full stderr[21:21:22] This is snippy 4.6.0
[21:21:22] Written by Torsten Seemann
[21:21:22] Obtained from https://github.com/tseemann/snippy
[21:21:22] Detected operating system: linux
[21:21:22] Enabling bundled linux tools.
[21:21:22] Found bwa - /usr/local/bin/bwa
[21:21:22] Found bcftools - /usr/local/bin/bcftools
[21:21:22] Found samtools - /usr/local/bin/samtools
[21:21:22] Found java - /usr/local/bin/java
[21:21:22] Found snpEff - /usr/local/bin/snpEff
[21:21:22] Found samclip - /usr/local/bin/samclip
[21:21:22] Found seqtk - /usr/local/bin/seqtk
[21:21:22] Found parallel - /usr/local/bin/parallel
[21:21:22] Found freebayes - /usr/local/bin/freebayes
[21:21:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:21:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:21:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:21:22] Found vcfuniq - /usr/local/bin/vcfuniq
[21:21:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:21:22] Found gzip - /bin/gzip
[21:21:22] Found vt - /usr/local/bin/vt
[21:21:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:21:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:21:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:21:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:21:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:21:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:21:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:21:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:20:12] This is snippy 4.6.0Show full stderr[21:20:12] This is snippy 4.6.0
[21:20:12] Written by Torsten Seemann
[21:20:12] Obtained from https://github.com/tseemann/snippy
[21:20:12] Detected operating system: linux
[21:20:12] Enabling bundled linux tools.
[21:20:12] Found bwa - /usr/local/bin/bwa
[21:20:12] Found bcftools - /usr/local/bin/bcftools
[21:20:12] Found samtools - /usr/local/bin/samtools
[21:20:12] Found java - /usr/local/bin/java
[21:20:12] Found snpEff - /usr/local/bin/snpEff
[21:20:12] Found samclip - /usr/local/bin/samclip
[21:20:12] Found seqtk - /usr/local/bin/seqtk
[21:20:12] Found parallel - /usr/local/bin/parallel
[21:20:12] Found freebayes - /usr/local/bin/freebayes
[21:20:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:20:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:20:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:20:12] Found vcfuniq - /usr/local/bin/vcfuniq
[21:20:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:20:12] Found gzip - /bin/gzip
[21:20:12] Found vt - /usr/local/bin/vt
[21:20:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:20:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:20:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:20:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:20:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:20:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:20:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:20:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:29:59] This is snippy 4.6.0Show full stderr[21:29:59] This is snippy 4.6.0
[21:29:59] Written by Torsten Seemann
[21:29:59] Obtained from https://github.com/tseemann/snippy
[21:29:59] Detected operating system: linux
[21:29:59] Enabling bundled linux tools.
[21:29:59] Found bwa - /usr/local/bin/bwa
[21:29:59] Found bcftools - /usr/local/bin/bcftools
[21:29:59] Found samtools - /usr/local/bin/samtools
[21:29:59] Found java - /usr/local/bin/java
[21:29:59] Found snpEff - /usr/local/bin/snpEff
[21:29:59] Found samclip - /usr/local/bin/samclip
[21:29:59] Found seqtk - /usr/local/bin/seqtk
[21:29:59] Found parallel - /usr/local/bin/parallel
[21:29:59] Found freebayes - /usr/local/bin/freebayes
[21:29:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:29:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:29:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:29:59] Found vcfuniq - /usr/local/bin/vcfuniq
[21:29:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:29:59] Found gzip - /bin/gzip
[21:29:59] Found vt - /usr/local/bin/vt
[21:29:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:29:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:29:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:29:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:29:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:30:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:30:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:30:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:38:27] This is snippy 4.6.0Show full stderr[21:38:27] This is snippy 4.6.0
[21:38:27] Written by Torsten Seemann
[21:38:27] Obtained from https://github.com/tseemann/snippy
[21:38:27] Detected operating system: linux
[21:38:27] Enabling bundled linux tools.
[21:38:27] Found bwa - /usr/local/bin/bwa
[21:38:27] Found bcftools - /usr/local/bin/bcftools
[21:38:27] Found samtools - /usr/local/bin/samtools
[21:38:27] Found java - /usr/local/bin/java
[21:38:27] Found snpEff - /usr/local/bin/snpEff
[21:38:27] Found samclip - /usr/local/bin/samclip
[21:38:28] Found seqtk - /usr/local/bin/seqtk
[21:38:28] Found parallel - /usr/local/bin/parallel
[21:38:28] Found freebayes - /usr/local/bin/freebayes
[21:38:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:38:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:38:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:38:28] Found vcfuniq - /usr/local/bin/vcfuniq
[21:38:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:38:28] Found gzip - /bin/gzip
[21:38:28] Found vt - /usr/local/bin/vt
[21:38:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:38:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:38:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:38:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:38:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:38:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:38:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:38:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:46:28] This is snippy 4.6.0Show full stderr[21:46:28] This is snippy 4.6.0
[21:46:28] Written by Torsten Seemann
[21:46:28] Obtained from https://github.com/tseemann/snippy
[21:46:28] Detected operating system: linux
[21:46:28] Enabling bundled linux tools.
[21:46:28] Found bwa - /usr/local/bin/bwa
[21:46:28] Found bcftools - /usr/local/bin/bcftools
[21:46:28] Found samtools - /usr/local/bin/samtools
[21:46:28] Found java - /usr/local/bin/java
[21:46:28] Found snpEff - /usr/local/bin/snpEff
[21:46:28] Found samclip - /usr/local/bin/samclip
[21:46:28] Found seqtk - /usr/local/bin/seqtk
[21:46:28] Found parallel - /usr/local/bin/parallel
[21:46:28] Found freebayes - /usr/local/bin/freebayes
[21:46:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:46:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:46:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:46:28] Found vcfuniq - /usr/local/bin/vcfuniq
[21:46:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:46:28] Found gzip - /bin/gzip
[21:46:28] Found vt - /usr/local/bin/vt
[21:46:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:46:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:46:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:46:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:46:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:46:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:46:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:46:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:46:47] This is snippy 4.6.0Show full stderr[21:46:47] This is snippy 4.6.0
[21:46:47] Written by Torsten Seemann
[21:46:47] Obtained from https://github.com/tseemann/snippy
[21:46:47] Detected operating system: linux
[21:46:47] Enabling bundled linux tools.
[21:46:47] Found bwa - /usr/local/bin/bwa
[21:46:47] Found bcftools - /usr/local/bin/bcftools
[21:46:47] Found samtools - /usr/local/bin/samtools
[21:46:47] Found java - /usr/local/bin/java
[21:46:47] Found snpEff - /usr/local/bin/snpEff
[21:46:47] Found samclip - /usr/local/bin/samclip
[21:46:47] Found seqtk - /usr/local/bin/seqtk
[21:46:47] Found parallel - /usr/local/bin/parallel
[21:46:47] Found freebayes - /usr/local/bin/freebayes
[21:46:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:46:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:46:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:46:47] Found vcfuniq - /usr/local/bin/vcfuniq
[21:46:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:46:47] Found gzip - /bin/gzip
[21:46:47] Found vt - /usr/local/bin/vt
[21:46:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:46:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:46:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:46:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:46:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:46:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:46:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:46:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:54:29] This is snippy 4.6.0Show full stderr[21:54:29] This is snippy 4.6.0
[21:54:29] Written by Torsten Seemann
[21:54:29] Obtained from https://github.com/tseemann/snippy
[21:54:29] Detected operating system: linux
[21:54:29] Enabling bundled linux tools.
[21:54:29] Found bwa - /usr/local/bin/bwa
[21:54:29] Found bcftools - /usr/local/bin/bcftools
[21:54:29] Found samtools - /usr/local/bin/samtools
[21:54:29] Found java - /usr/local/bin/java
[21:54:29] Found snpEff - /usr/local/bin/snpEff
[21:54:29] Found samclip - /usr/local/bin/samclip
[21:54:29] Found seqtk - /usr/local/bin/seqtk
[21:54:29] Found parallel - /usr/local/bin/parallel
[21:54:29] Found freebayes - /usr/local/bin/freebayes
[21:54:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:54:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:54:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:54:29] Found vcfuniq - /usr/local/bin/vcfuniq
[21:54:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:54:29] Found gzip - /bin/gzip
[21:54:29] Found vt - /usr/local/bin/vt
[21:54:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:54:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:54:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:54:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:54:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:54:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:54:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:54:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:28:00] This is snippy 4.6.0Show full stderr[22:28:00] This is snippy 4.6.0
[22:28:00] Written by Torsten Seemann
[22:28:00] Obtained from https://github.com/tseemann/snippy
[22:28:00] Detected operating system: linux
[22:28:00] Enabling bundled linux tools.
[22:28:00] Found bwa - /usr/local/bin/bwa
[22:28:00] Found bcftools - /usr/local/bin/bcftools
[22:28:00] Found samtools - /usr/local/bin/samtools
[22:28:00] Found java - /usr/local/bin/java
[22:28:00] Found snpEff - /usr/local/bin/snpEff
[22:28:00] Found samclip - /usr/local/bin/samclip
[22:28:00] Found seqtk - /usr/local/bin/seqtk
[22:28:00] Found parallel - /usr/local/bin/parallel
[22:28:00] Found freebayes - /usr/local/bin/freebayes
[22:28:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:28:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:28:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:28:00] Found vcfuniq - /usr/local/bin/vcfuniq
[22:28:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:28:00] Found gzip - /bin/gzip
[22:28:00] Found vt - /usr/local/bin/vt
[22:28:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:28:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:28:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:28:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:28:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:28:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:28:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:28:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:28:29] This is snippy 4.6.0Show full stderr[22:28:29] This is snippy 4.6.0
[22:28:29] Written by Torsten Seemann
[22:28:29] Obtained from https://github.com/tseemann/snippy
[22:28:29] Detected operating system: linux
[22:28:29] Enabling bundled linux tools.
[22:28:29] Found bwa - /usr/local/bin/bwa
[22:28:29] Found bcftools - /usr/local/bin/bcftools
[22:28:29] Found samtools - /usr/local/bin/samtools
[22:28:29] Found java - /usr/local/bin/java
[22:28:29] Found snpEff - /usr/local/bin/snpEff
[22:28:29] Found samclip - /usr/local/bin/samclip
[22:28:29] Found seqtk - /usr/local/bin/seqtk
[22:28:29] Found parallel - /usr/local/bin/parallel
[22:28:29] Found freebayes - /usr/local/bin/freebayes
[22:28:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:28:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:28:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:28:29] Found vcfuniq - /usr/local/bin/vcfuniq
[22:28:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:28:29] Found gzip - /bin/gzip
[22:28:29] Found vt - /usr/local/bin/vt
[22:28:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:28:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:28:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:28:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:28:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:28:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:28:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:28:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:01:35] This is snippy 4.6.0Show full stderr[23:01:35] This is snippy 4.6.0
[23:01:35] Written by Torsten Seemann
[23:01:35] Obtained from https://github.com/tseemann/snippy
[23:01:35] Detected operating system: linux
[23:01:35] Enabling bundled linux tools.
[23:01:35] Found bwa - /usr/local/bin/bwa
[23:01:35] Found bcftools - /usr/local/bin/bcftools
[23:01:35] Found samtools - /usr/local/bin/samtools
[23:01:35] Found java - /usr/local/bin/java
[23:01:35] Found snpEff - /usr/local/bin/snpEff
[23:01:35] Found samclip - /usr/local/bin/samclip
[23:01:35] Found seqtk - /usr/local/bin/seqtk
[23:01:35] Found parallel - /usr/local/bin/parallel
[23:01:35] Found freebayes - /usr/local/bin/freebayes
[23:01:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:01:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:01:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:01:35] Found vcfuniq - /usr/local/bin/vcfuniq
[23:01:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:01:35] Found gzip - /bin/gzip
[23:01:35] Found vt - /usr/local/bin/vt
[23:01:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:01:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:01:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:01:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:01:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:01:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:01:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:01:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:01:50] This is snippy 4.6.0Show full stderr[23:01:50] This is snippy 4.6.0
[23:01:50] Written by Torsten Seemann
[23:01:50] Obtained from https://github.com/tseemann/snippy
[23:01:50] Detected operating system: linux
[23:01:50] Enabling bundled linux tools.
[23:01:50] Found bwa - /usr/local/bin/bwa
[23:01:50] Found bcftools - /usr/local/bin/bcftools
[23:01:50] Found samtools - /usr/local/bin/samtools
[23:01:50] Found java - /usr/local/bin/java
[23:01:50] Found snpEff - /usr/local/bin/snpEff
[23:01:50] Found samclip - /usr/local/bin/samclip
[23:01:50] Found seqtk - /usr/local/bin/seqtk
[23:01:50] Found parallel - /usr/local/bin/parallel
[23:01:50] Found freebayes - /usr/local/bin/freebayes
[23:01:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:01:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:01:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:01:50] Found vcfuniq - /usr/local/bin/vcfuniq
[23:01:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:01:50] Found gzip - /bin/gzip
[23:01:50] Found vt - /usr/local/bin/vt
[23:01:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:01:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:01:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:01:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:01:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:01:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:01:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:01:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:00:10] This is snippy 4.6.0Show full stderr[02:00:10] This is snippy 4.6.0
[02:00:10] Written by Torsten Seemann
[02:00:10] Obtained from https://github.com/tseemann/snippy
[02:00:10] Detected operating system: linux
[02:00:10] Enabling bundled linux tools.
[02:00:10] Found bwa - /usr/local/bin/bwa
[02:00:10] Found bcftools - /usr/local/bin/bcftools
[02:00:10] Found samtools - /usr/local/bin/samtools
[02:00:10] Found java - /usr/local/bin/java
[02:00:10] Found snpEff - /usr/local/bin/snpEff
[02:00:10] Found samclip - /usr/local/bin/samclip
[02:00:10] Found seqtk - /usr/local/bin/seqtk
[02:00:10] Found parallel - /usr/local/bin/parallel
[02:00:10] Found freebayes - /usr/local/bin/freebayes
[02:00:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:00:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:00:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:00:10] Found vcfuniq - /usr/local/bin/vcfuniq
[02:00:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:00:10] Found gzip - /bin/gzip
[02:00:10] Found vt - /usr/local/bin/vt
[02:00:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:00:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:00:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:00:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:00:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:00:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:00:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:00:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:51:18] This is snippy 4.6.0Show full stderr[18:51:18] This is snippy 4.6.0
[18:51:18] Written by Torsten Seemann
[18:51:18] Obtained from https://github.com/tseemann/snippy
[18:51:18] Detected operating system: linux
[18:51:18] Enabling bundled linux tools.
[18:51:18] Found bwa - /usr/local/bin/bwa
[18:51:18] Found bcftools - /usr/local/bin/bcftools
[18:51:18] Found samtools - /usr/local/bin/samtools
[18:51:18] Found java - /usr/local/bin/java
[18:51:18] Found snpEff - /usr/local/bin/snpEff
[18:51:18] Found samclip - /usr/local/bin/samclip
[18:51:18] Found seqtk - /usr/local/bin/seqtk
[18:51:18] Found parallel - /usr/local/bin/parallel
[18:51:18] Found freebayes - /usr/local/bin/freebayes
[18:51:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:51:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:51:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:51:18] Found vcfuniq - /usr/local/bin/vcfuniq
[18:51:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:51:18] Found gzip - /bin/gzip
[18:51:18] Found vt - /usr/local/bin/vt
[18:51:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:51:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:51:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:51:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:51:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:51:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:51:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:51:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:17:23] This is snippy 4.6.0Show full stderr[17:17:23] This is snippy 4.6.0
[17:17:23] Written by Torsten Seemann
[17:17:23] Obtained from https://github.com/tseemann/snippy
[17:17:23] Detected operating system: linux
[17:17:23] Enabling bundled linux tools.
[17:17:23] Found bwa - /usr/local/bin/bwa
[17:17:23] Found bcftools - /usr/local/bin/bcftools
[17:17:23] Found samtools - /usr/local/bin/samtools
[17:17:23] Found java - /usr/local/bin/java
[17:17:23] Found snpEff - /usr/local/bin/snpEff
[17:17:23] Found samclip - /usr/local/bin/samclip
[17:17:23] Found seqtk - /usr/local/bin/seqtk
[17:17:23] Found parallel - /usr/local/bin/parallel
[17:17:23] Found freebayes - /usr/local/bin/freebayes
[17:17:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:17:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:17:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:17:23] Found vcfuniq - /usr/local/bin/vcfuniq
[17:17:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:17:23] Found gzip - /bin/gzip
[17:17:23] Found vt - /usr/local/bin/vt
[17:17:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:17:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:17:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:17:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:17:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:17:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:17:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:17:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:17:12] This is snippy 4.6.0Show full stderr[17:17:12] This is snippy 4.6.0
[17:17:12] Written by Torsten Seemann
[17:17:12] Obtained from https://github.com/tseemann/snippy
[17:17:12] Detected operating system: linux
[17:17:12] Enabling bundled linux tools.
[17:17:12] Found bwa - /usr/local/bin/bwa
[17:17:12] Found bcftools - /usr/local/bin/bcftools
[17:17:12] Found samtools - /usr/local/bin/samtools
[17:17:12] Found java - /usr/local/bin/java
[17:17:12] Found snpEff - /usr/local/bin/snpEff
[17:17:12] Found samclip - /usr/local/bin/samclip
[17:17:12] Found seqtk - /usr/local/bin/seqtk
[17:17:12] Found parallel - /usr/local/bin/parallel
[17:17:12] Found freebayes - /usr/local/bin/freebayes
[17:17:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:17:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:17:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:17:12] Found vcfuniq - /usr/local/bin/vcfuniq
[17:17:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:17:12] Found gzip - /bin/gzip
[17:17:12] Found vt - /usr/local/bin/vt
[17:17:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:17:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:17:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:17:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:17:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:17:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:17:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:17:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:00:26] This is snippy 4.6.0Show full stderr[02:00:26] This is snippy 4.6.0
[02:00:26] Written by Torsten Seemann
[02:00:26] Obtained from https://github.com/tseemann/snippy
[02:00:26] Detected operating system: linux
[02:00:26] Enabling bundled linux tools.
[02:00:26] Found bwa - /usr/local/bin/bwa
[02:00:26] Found bcftools - /usr/local/bin/bcftools
[02:00:26] Found samtools - /usr/local/bin/samtools
[02:00:26] Found java - /usr/local/bin/java
[02:00:26] Found snpEff - /usr/local/bin/snpEff
[02:00:26] Found samclip - /usr/local/bin/samclip
[02:00:26] Found seqtk - /usr/local/bin/seqtk
[02:00:26] Found parallel - /usr/local/bin/parallel
[02:00:26] Found freebayes - /usr/local/bin/freebayes
[02:00:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:00:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:00:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:00:26] Found vcfuniq - /usr/local/bin/vcfuniq
[02:00:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:00:26] Found gzip - /bin/gzip
[02:00:26] Found vt - /usr/local/bin/vt
[02:00:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:00:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:00:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:00:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:00:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:00:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:00:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:00:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:03:27] This is snippy 4.6.0Show full stderr[21:03:27] This is snippy 4.6.0
[21:03:27] Written by Torsten Seemann
[21:03:27] Obtained from https://github.com/tseemann/snippy
[21:03:27] Detected operating system: linux
[21:03:27] Enabling bundled linux tools.
[21:03:27] Found bwa - /usr/local/bin/bwa
[21:03:27] Found bcftools - /usr/local/bin/bcftools
[21:03:27] Found samtools - /usr/local/bin/samtools
[21:03:27] Found java - /usr/local/bin/java
[21:03:27] Found snpEff - /usr/local/bin/snpEff
[21:03:27] Found samclip - /usr/local/bin/samclip
[21:03:27] Found seqtk - /usr/local/bin/seqtk
[21:03:27] Found parallel - /usr/local/bin/parallel
[21:03:27] Found freebayes - /usr/local/bin/freebayes
[21:03:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:03:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:03:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:03:27] Found vcfuniq - /usr/local/bin/vcfuniq
[21:03:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:03:27] Found gzip - /bin/gzip
[21:03:27] Found vt - /usr/local/bin/vt
[21:03:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:03:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:03:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:03:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:03:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:03:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:03:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:03:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:44:05] This is snippy 4.6.0Show full stderr[00:44:05] This is snippy 4.6.0
[00:44:05] Written by Torsten Seemann
[00:44:05] Obtained from https://github.com/tseemann/snippy
[00:44:05] Detected operating system: linux
[00:44:05] Enabling bundled linux tools.
[00:44:05] Found bwa - /usr/local/bin/bwa
[00:44:05] Found bcftools - /usr/local/bin/bcftools
[00:44:05] Found samtools - /usr/local/bin/samtools
[00:44:05] Found java - /usr/local/bin/java
[00:44:05] Found snpEff - /usr/local/bin/snpEff
[00:44:05] Found samclip - /usr/local/bin/samclip
[00:44:05] Found seqtk - /usr/local/bin/seqtk
[00:44:05] Found parallel - /usr/local/bin/parallel
[00:44:05] Found freebayes - /usr/local/bin/freebayes
[00:44:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:44:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:44:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:44:05] Found vcfuniq - /usr/local/bin/vcfuniq
[00:44:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:44:05] Found gzip - /bin/gzip
[00:44:05] Found vt - /usr/local/bin/vt
[00:44:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:44:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:44:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:44:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:44:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:44:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:44:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:44:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:00:48] This is snippy 4.6.0Show full stderr[02:00:48] This is snippy 4.6.0
[02:00:48] Written by Torsten Seemann
[02:00:48] Obtained from https://github.com/tseemann/snippy
[02:00:48] Detected operating system: linux
[02:00:48] Enabling bundled linux tools.
[02:00:48] Found bwa - /usr/local/bin/bwa
[02:00:48] Found bcftools - /usr/local/bin/bcftools
[02:00:48] Found samtools - /usr/local/bin/samtools
[02:00:48] Found java - /usr/local/bin/java
[02:00:48] Found snpEff - /usr/local/bin/snpEff
[02:00:48] Found samclip - /usr/local/bin/samclip
[02:00:48] Found seqtk - /usr/local/bin/seqtk
[02:00:48] Found parallel - /usr/local/bin/parallel
[02:00:48] Found freebayes - /usr/local/bin/freebayes
[02:00:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:00:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:00:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:00:48] Found vcfuniq - /usr/local/bin/vcfuniq
[02:00:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:00:48] Found gzip - /bin/gzip
[02:00:48] Found vt - /usr/local/bin/vt
[02:00:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:00:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:00:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:00:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:00:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:00:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:00:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:00:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:04:17] This is snippy 4.6.0Show full stderr[21:04:17] This is snippy 4.6.0
[21:04:17] Written by Torsten Seemann
[21:04:17] Obtained from https://github.com/tseemann/snippy
[21:04:17] Detected operating system: linux
[21:04:17] Enabling bundled linux tools.
[21:04:17] Found bwa - /usr/local/bin/bwa
[21:04:17] Found bcftools - /usr/local/bin/bcftools
[21:04:17] Found samtools - /usr/local/bin/samtools
[21:04:17] Found java - /usr/local/bin/java
[21:04:17] Found snpEff - /usr/local/bin/snpEff
[21:04:18] Found samclip - /usr/local/bin/samclip
[21:04:18] Found seqtk - /usr/local/bin/seqtk
[21:04:18] Found parallel - /usr/local/bin/parallel
[21:04:18] Found freebayes - /usr/local/bin/freebayes
[21:04:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:04:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:04:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:04:18] Found vcfuniq - /usr/local/bin/vcfuniq
[21:04:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:04:18] Found gzip - /bin/gzip
[21:04:18] Found vt - /usr/local/bin/vt
[21:04:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:04:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:04:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:04:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:04:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:04:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:04:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:04:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:38:47] This is snippy 4.6.0Show full stderr[21:38:47] This is snippy 4.6.0
[21:38:47] Written by Torsten Seemann
[21:38:47] Obtained from https://github.com/tseemann/snippy
[21:38:47] Detected operating system: linux
[21:38:47] Enabling bundled linux tools.
[21:38:47] Found bwa - /usr/local/bin/bwa
[21:38:47] Found bcftools - /usr/local/bin/bcftools
[21:38:47] Found samtools - /usr/local/bin/samtools
[21:38:47] Found java - /usr/local/bin/java
[21:38:47] Found snpEff - /usr/local/bin/snpEff
[21:38:47] Found samclip - /usr/local/bin/samclip
[21:38:47] Found seqtk - /usr/local/bin/seqtk
[21:38:47] Found parallel - /usr/local/bin/parallel
[21:38:47] Found freebayes - /usr/local/bin/freebayes
[21:38:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:38:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:38:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:38:47] Found vcfuniq - /usr/local/bin/vcfuniq
[21:38:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:38:47] Found gzip - /bin/gzip
[21:38:47] Found vt - /usr/local/bin/vt
[21:38:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:38:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:38:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:38:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:38:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:38:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:38:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:38:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:01:16] This is snippy 4.6.0Show full stderr[23:01:16] This is snippy 4.6.0
[23:01:16] Written by Torsten Seemann
[23:01:16] Obtained from https://github.com/tseemann/snippy
[23:01:16] Detected operating system: linux
[23:01:16] Enabling bundled linux tools.
[23:01:16] Found bwa - /usr/local/bin/bwa
[23:01:16] Found bcftools - /usr/local/bin/bcftools
[23:01:16] Found samtools - /usr/local/bin/samtools
[23:01:16] Found java - /usr/local/bin/java
[23:01:16] Found snpEff - /usr/local/bin/snpEff
[23:01:16] Found samclip - /usr/local/bin/samclip
[23:01:16] Found seqtk - /usr/local/bin/seqtk
[23:01:16] Found parallel - /usr/local/bin/parallel
[23:01:16] Found freebayes - /usr/local/bin/freebayes
[23:01:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:01:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:01:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:01:16] Found vcfuniq - /usr/local/bin/vcfuniq
[23:01:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:01:16] Found gzip - /bin/gzip
[23:01:16] Found vt - /usr/local/bin/vt
[23:01:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:01:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:01:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:01:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:01:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:01:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:01:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:01:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:21:34] This is snippy 4.6.0Show full stderr[21:21:34] This is snippy 4.6.0
[21:21:34] Written by Torsten Seemann
[21:21:34] Obtained from https://github.com/tseemann/snippy
[21:21:34] Detected operating system: linux
[21:21:34] Enabling bundled linux tools.
[21:21:34] Found bwa - /usr/local/bin/bwa
[21:21:34] Found bcftools - /usr/local/bin/bcftools
[21:21:34] Found samtools - /usr/local/bin/samtools
[21:21:34] Found java - /usr/local/bin/java
[21:21:34] Found snpEff - /usr/local/bin/snpEff
[21:21:34] Found samclip - /usr/local/bin/samclip
[21:21:34] Found seqtk - /usr/local/bin/seqtk
[21:21:34] Found parallel - /usr/local/bin/parallel
[21:21:34] Found freebayes - /usr/local/bin/freebayes
[21:21:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:21:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:21:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:21:34] Found vcfuniq - /usr/local/bin/vcfuniq
[21:21:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:21:34] Found gzip - /bin/gzip
[21:21:34] Found vt - /usr/local/bin/vt
[21:21:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:21:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:21:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:21:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:21:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:21:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:21:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:21:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:08:34] This is snippy 4.6.0Show full stderr[02:08:34] This is snippy 4.6.0
[02:08:34] Written by Torsten Seemann
[02:08:34] Obtained from https://github.com/tseemann/snippy
[02:08:34] Detected operating system: linux
[02:08:34] Enabling bundled linux tools.
[02:08:34] Found bwa - /usr/local/bin/bwa
[02:08:34] Found bcftools - /usr/local/bin/bcftools
[02:08:34] Found samtools - /usr/local/bin/samtools
[02:08:34] Found java - /usr/local/bin/java
[02:08:34] Found snpEff - /usr/local/bin/snpEff
[02:08:34] Found samclip - /usr/local/bin/samclip
[02:08:34] Found seqtk - /usr/local/bin/seqtk
[02:08:34] Found parallel - /usr/local/bin/parallel
[02:08:34] Found freebayes - /usr/local/bin/freebayes
[02:08:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:08:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:08:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:08:34] Found vcfuniq - /usr/local/bin/vcfuniq
[02:08:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:08:34] Found gzip - /bin/gzip
[02:08:34] Found vt - /usr/local/bin/vt
[02:08:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:08:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:08:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:08:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:08:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:08:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:08:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:08:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:09:19] This is snippy 4.6.0Show full stderr[02:09:19] This is snippy 4.6.0
[02:09:19] Written by Torsten Seemann
[02:09:19] Obtained from https://github.com/tseemann/snippy
[02:09:19] Detected operating system: linux
[02:09:19] Enabling bundled linux tools.
[02:09:19] Found bwa - /usr/local/bin/bwa
[02:09:19] Found bcftools - /usr/local/bin/bcftools
[02:09:19] Found samtools - /usr/local/bin/samtools
[02:09:19] Found java - /usr/local/bin/java
[02:09:19] Found snpEff - /usr/local/bin/snpEff
[02:09:19] Found samclip - /usr/local/bin/samclip
[02:09:19] Found seqtk - /usr/local/bin/seqtk
[02:09:19] Found parallel - /usr/local/bin/parallel
[02:09:19] Found freebayes - /usr/local/bin/freebayes
[02:09:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:09:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:09:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:09:19] Found vcfuniq - /usr/local/bin/vcfuniq
[02:09:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:09:19] Found gzip - /bin/gzip
[02:09:19] Found vt - /usr/local/bin/vt
[02:09:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:09:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:09:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:09:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:09:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:09:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:09:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:09:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:09:38] This is snippy 4.6.0Show full stderr[02:09:38] This is snippy 4.6.0
[02:09:38] Written by Torsten Seemann
[02:09:38] Obtained from https://github.com/tseemann/snippy
[02:09:38] Detected operating system: linux
[02:09:38] Enabling bundled linux tools.
[02:09:38] Found bwa - /usr/local/bin/bwa
[02:09:38] Found bcftools - /usr/local/bin/bcftools
[02:09:38] Found samtools - /usr/local/bin/samtools
[02:09:38] Found java - /usr/local/bin/java
[02:09:38] Found snpEff - /usr/local/bin/snpEff
[02:09:38] Found samclip - /usr/local/bin/samclip
[02:09:38] Found seqtk - /usr/local/bin/seqtk
[02:09:38] Found parallel - /usr/local/bin/parallel
[02:09:38] Found freebayes - /usr/local/bin/freebayes
[02:09:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:09:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:09:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:09:38] Found vcfuniq - /usr/local/bin/vcfuniq
[02:09:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:09:38] Found gzip - /bin/gzip
[02:09:38] Found vt - /usr/local/bin/vt
[02:09:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:09:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:09:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:09:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:09:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:09:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:09:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:09:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:20:39] This is snippy 4.6.0Show full stderr[21:20:39] This is snippy 4.6.0
[21:20:39] Written by Torsten Seemann
[21:20:39] Obtained from https://github.com/tseemann/snippy
[21:20:39] Detected operating system: linux
[21:20:39] Enabling bundled linux tools.
[21:20:39] Found bwa - /usr/local/bin/bwa
[21:20:39] Found bcftools - /usr/local/bin/bcftools
[21:20:39] Found samtools - /usr/local/bin/samtools
[21:20:39] Found java - /usr/local/bin/java
[21:20:39] Found snpEff - /usr/local/bin/snpEff
[21:20:39] Found samclip - /usr/local/bin/samclip
[21:20:39] Found seqtk - /usr/local/bin/seqtk
[21:20:39] Found parallel - /usr/local/bin/parallel
[21:20:39] Found freebayes - /usr/local/bin/freebayes
[21:20:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:20:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:20:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:20:39] Found vcfuniq - /usr/local/bin/vcfuniq
[21:20:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:20:39] Found gzip - /bin/gzip
[21:20:39] Found vt - /usr/local/bin/vt
[21:20:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:20:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:20:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:20:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:20:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:20:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:20:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:20:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:42:26] This is snippy 4.6.0Show full stderr[17:42:26] This is snippy 4.6.0
[17:42:26] Written by Torsten Seemann
[17:42:26] Obtained from https://github.com/tseemann/snippy
[17:42:26] Detected operating system: linux
[17:42:26] Enabling bundled linux tools.
[17:42:26] Found bwa - /usr/local/bin/bwa
[17:42:26] Found bcftools - /usr/local/bin/bcftools
[17:42:26] Found samtools - /usr/local/bin/samtools
[17:42:26] Found java - /usr/local/bin/java
[17:42:26] Found snpEff - /usr/local/bin/snpEff
[17:42:26] Found samclip - /usr/local/bin/samclip
[17:42:26] Found seqtk - /usr/local/bin/seqtk
[17:42:26] Found parallel - /usr/local/bin/parallel
[17:42:26] Found freebayes - /usr/local/bin/freebayes
[17:42:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:42:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:42:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:42:26] Found vcfuniq - /usr/local/bin/vcfuniq
[17:42:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:42:27] Found gzip - /bin/gzip
[17:42:27] Found vt - /usr/local/bin/vt
[17:42:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:42:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:42:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:42:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:42:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:42:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:42:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:42:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:09:47] This is snippy 4.6.0Show full stderr[01:09:47] This is snippy 4.6.0
[01:09:47] Written by Torsten Seemann
[01:09:47] Obtained from https://github.com/tseemann/snippy
[01:09:47] Detected operating system: linux
[01:09:47] Enabling bundled linux tools.
[01:09:47] Found bwa - /usr/local/bin/bwa
[01:09:47] Found bcftools - /usr/local/bin/bcftools
[01:09:47] Found samtools - /usr/local/bin/samtools
[01:09:47] Found java - /usr/local/bin/java
[01:09:47] Found snpEff - /usr/local/bin/snpEff
[01:09:47] Found samclip - /usr/local/bin/samclip
[01:09:47] Found seqtk - /usr/local/bin/seqtk
[01:09:47] Found parallel - /usr/local/bin/parallel
[01:09:47] Found freebayes - /usr/local/bin/freebayes
[01:09:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:09:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:09:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:09:47] Found vcfuniq - /usr/local/bin/vcfuniq
[01:09:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:09:47] Found gzip - /bin/gzip
[01:09:47] Found vt - /usr/local/bin/vt
[01:09:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:09:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:09:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:09:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:09:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:09:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:09:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:09:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:18:17] This is snippy 4.6.0Show full stderr[01:18:17] This is snippy 4.6.0
[01:18:17] Written by Torsten Seemann
[01:18:17] Obtained from https://github.com/tseemann/snippy
[01:18:17] Detected operating system: linux
[01:18:17] Enabling bundled linux tools.
[01:18:17] Found bwa - /usr/local/bin/bwa
[01:18:17] Found bcftools - /usr/local/bin/bcftools
[01:18:17] Found samtools - /usr/local/bin/samtools
[01:18:17] Found java - /usr/local/bin/java
[01:18:17] Found snpEff - /usr/local/bin/snpEff
[01:18:17] Found samclip - /usr/local/bin/samclip
[01:18:17] Found seqtk - /usr/local/bin/seqtk
[01:18:17] Found parallel - /usr/local/bin/parallel
[01:18:17] Found freebayes - /usr/local/bin/freebayes
[01:18:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:18:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:18:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:18:17] Found vcfuniq - /usr/local/bin/vcfuniq
[01:18:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:18:17] Found gzip - /bin/gzip
[01:18:17] Found vt - /usr/local/bin/vt
[01:18:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:18:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:18:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:18:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:18:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:18:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:18:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:18:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:25:58] This is snippy 4.6.0Show full stderr[01:25:58] This is snippy 4.6.0
[01:25:58] Written by Torsten Seemann
[01:25:58] Obtained from https://github.com/tseemann/snippy
[01:25:58] Detected operating system: linux
[01:25:58] Enabling bundled linux tools.
[01:25:58] Found bwa - /usr/local/bin/bwa
[01:25:58] Found bcftools - /usr/local/bin/bcftools
[01:25:58] Found samtools - /usr/local/bin/samtools
[01:25:58] Found java - /usr/local/bin/java
[01:25:58] Found snpEff - /usr/local/bin/snpEff
[01:25:58] Found samclip - /usr/local/bin/samclip
[01:25:58] Found seqtk - /usr/local/bin/seqtk
[01:25:58] Found parallel - /usr/local/bin/parallel
[01:25:58] Found freebayes - /usr/local/bin/freebayes
[01:25:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:25:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:25:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:25:58] Found vcfuniq - /usr/local/bin/vcfuniq
[01:25:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:25:58] Found gzip - /bin/gzip
[01:25:58] Found vt - /usr/local/bin/vt
[01:25:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:25:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:25:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:25:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:25:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:25:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:25:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:25:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:26:13] This is snippy 4.6.0Show full stderr[01:26:13] This is snippy 4.6.0
[01:26:13] Written by Torsten Seemann
[01:26:13] Obtained from https://github.com/tseemann/snippy
[01:26:13] Detected operating system: linux
[01:26:13] Enabling bundled linux tools.
[01:26:13] Found bwa - /usr/local/bin/bwa
[01:26:13] Found bcftools - /usr/local/bin/bcftools
[01:26:13] Found samtools - /usr/local/bin/samtools
[01:26:13] Found java - /usr/local/bin/java
[01:26:13] Found snpEff - /usr/local/bin/snpEff
[01:26:13] Found samclip - /usr/local/bin/samclip
[01:26:13] Found seqtk - /usr/local/bin/seqtk
[01:26:13] Found parallel - /usr/local/bin/parallel
[01:26:13] Found freebayes - /usr/local/bin/freebayes
[01:26:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:26:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:26:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:26:13] Found vcfuniq - /usr/local/bin/vcfuniq
[01:26:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:26:13] Found gzip - /bin/gzip
[01:26:13] Found vt - /usr/local/bin/vt
[01:26:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:26:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:26:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:26:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:26:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:26:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:26:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:26:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:35:17] This is snippy 4.6.0Show full stderr[01:35:17] This is snippy 4.6.0
[01:35:17] Written by Torsten Seemann
[01:35:17] Obtained from https://github.com/tseemann/snippy
[01:35:17] Detected operating system: linux
[01:35:17] Enabling bundled linux tools.
[01:35:17] Found bwa - /usr/local/bin/bwa
[01:35:17] Found bcftools - /usr/local/bin/bcftools
[01:35:17] Found samtools - /usr/local/bin/samtools
[01:35:17] Found java - /usr/local/bin/java
[01:35:17] Found snpEff - /usr/local/bin/snpEff
[01:35:17] Found samclip - /usr/local/bin/samclip
[01:35:17] Found seqtk - /usr/local/bin/seqtk
[01:35:18] Found parallel - /usr/local/bin/parallel
[01:35:18] Found freebayes - /usr/local/bin/freebayes
[01:35:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:35:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:35:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:35:18] Found vcfuniq - /usr/local/bin/vcfuniq
[01:35:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:35:18] Found gzip - /bin/gzip
[01:35:18] Found vt - /usr/local/bin/vt
[01:35:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:35:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:35:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:35:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:35:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:35:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:35:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:35:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:50:59] This is snippy 4.6.0Show full stderr[01:50:59] This is snippy 4.6.0
[01:50:59] Written by Torsten Seemann
[01:50:59] Obtained from https://github.com/tseemann/snippy
[01:50:59] Detected operating system: linux
[01:50:59] Enabling bundled linux tools.
[01:50:59] Found bwa - /usr/local/bin/bwa
[01:51:00] Found bcftools - /usr/local/bin/bcftools
[01:51:00] Found samtools - /usr/local/bin/samtools
[01:51:00] Found java - /usr/local/bin/java
[01:51:00] Found snpEff - /usr/local/bin/snpEff
[01:51:00] Found samclip - /usr/local/bin/samclip
[01:51:00] Found seqtk - /usr/local/bin/seqtk
[01:51:00] Found parallel - /usr/local/bin/parallel
[01:51:00] Found freebayes - /usr/local/bin/freebayes
[01:51:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:51:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:51:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:51:00] Found vcfuniq - /usr/local/bin/vcfuniq
[01:51:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:51:00] Found gzip - /bin/gzip
[01:51:00] Found vt - /usr/local/bin/vt
[01:51:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:51:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:51:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:51:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:51:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:51:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:51:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:51:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:51:16] This is snippy 4.6.0Show full stderr[01:51:16] This is snippy 4.6.0
[01:51:16] Written by Torsten Seemann
[01:51:16] Obtained from https://github.com/tseemann/snippy
[01:51:16] Detected operating system: linux
[01:51:16] Enabling bundled linux tools.
[01:51:16] Found bwa - /usr/local/bin/bwa
[01:51:16] Found bcftools - /usr/local/bin/bcftools
[01:51:16] Found samtools - /usr/local/bin/samtools
[01:51:16] Found java - /usr/local/bin/java
[01:51:16] Found snpEff - /usr/local/bin/snpEff
[01:51:16] Found samclip - /usr/local/bin/samclip
[01:51:16] Found seqtk - /usr/local/bin/seqtk
[01:51:16] Found parallel - /usr/local/bin/parallel
[01:51:16] Found freebayes - /usr/local/bin/freebayes
[01:51:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:51:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:51:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:51:16] Found vcfuniq - /usr/local/bin/vcfuniq
[01:51:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:51:16] Found gzip - /bin/gzip
[01:51:16] Found vt - /usr/local/bin/vt
[01:51:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:51:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:51:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:51:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:51:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:51:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:51:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:51:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:05:50] This is snippy 4.6.0Show full stderr[20:05:50] This is snippy 4.6.0
[20:05:50] Written by Torsten Seemann
[20:05:50] Obtained from https://github.com/tseemann/snippy
[20:05:50] Detected operating system: linux
[20:05:50] Enabling bundled linux tools.
[20:05:50] Found bwa - /usr/local/bin/bwa
[20:05:50] Found bcftools - /usr/local/bin/bcftools
[20:05:50] Found samtools - /usr/local/bin/samtools
[20:05:50] Found java - /usr/local/bin/java
[20:05:50] Found snpEff - /usr/local/bin/snpEff
[20:05:50] Found samclip - /usr/local/bin/samclip
[20:05:50] Found seqtk - /usr/local/bin/seqtk
[20:05:50] Found parallel - /usr/local/bin/parallel
[20:05:50] Found freebayes - /usr/local/bin/freebayes
[20:05:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:05:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:05:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:05:50] Found vcfuniq - /usr/local/bin/vcfuniq
[20:05:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:05:50] Found gzip - /bin/gzip
[20:05:50] Found vt - /usr/local/bin/vt
[20:05:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:05:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:05:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:05:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:05:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:05:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:05:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:05:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:08:50] This is snippy 4.6.0Show full stderr[02:08:50] This is snippy 4.6.0
[02:08:50] Written by Torsten Seemann
[02:08:50] Obtained from https://github.com/tseemann/snippy
[02:08:50] Detected operating system: linux
[02:08:50] Enabling bundled linux tools.
[02:08:50] Found bwa - /usr/local/bin/bwa
[02:08:50] Found bcftools - /usr/local/bin/bcftools
[02:08:50] Found samtools - /usr/local/bin/samtools
[02:08:50] Found java - /usr/local/bin/java
[02:08:50] Found snpEff - /usr/local/bin/snpEff
[02:08:50] Found samclip - /usr/local/bin/samclip
[02:08:50] Found seqtk - /usr/local/bin/seqtk
[02:08:50] Found parallel - /usr/local/bin/parallel
[02:08:50] Found freebayes - /usr/local/bin/freebayes
[02:08:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:08:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:08:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:08:50] Found vcfuniq - /usr/local/bin/vcfuniq
[02:08:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:08:50] Found gzip - /bin/gzip
[02:08:50] Found vt - /usr/local/bin/vt
[02:08:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:08:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:08:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:08:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:08:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:08:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:08:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:08:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:09:04] This is snippy 4.6.0Show full stderr[02:09:04] This is snippy 4.6.0
[02:09:04] Written by Torsten Seemann
[02:09:04] Obtained from https://github.com/tseemann/snippy
[02:09:04] Detected operating system: linux
[02:09:04] Enabling bundled linux tools.
[02:09:04] Found bwa - /usr/local/bin/bwa
[02:09:04] Found bcftools - /usr/local/bin/bcftools
[02:09:04] Found samtools - /usr/local/bin/samtools
[02:09:04] Found java - /usr/local/bin/java
[02:09:04] Found snpEff - /usr/local/bin/snpEff
[02:09:04] Found samclip - /usr/local/bin/samclip
[02:09:04] Found seqtk - /usr/local/bin/seqtk
[02:09:04] Found parallel - /usr/local/bin/parallel
[02:09:04] Found freebayes - /usr/local/bin/freebayes
[02:09:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:09:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:09:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:09:04] Found vcfuniq - /usr/local/bin/vcfuniq
[02:09:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:09:04] Found gzip - /bin/gzip
[02:09:04] Found vt - /usr/local/bin/vt
[02:09:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:09:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:09:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:09:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:09:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:09:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:09:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:09:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:09:54] This is snippy 4.6.0Show full stderr[02:09:54] This is snippy 4.6.0
[02:09:54] Written by Torsten Seemann
[02:09:54] Obtained from https://github.com/tseemann/snippy
[02:09:54] Detected operating system: linux
[02:09:54] Enabling bundled linux tools.
[02:09:54] Found bwa - /usr/local/bin/bwa
[02:09:54] Found bcftools - /usr/local/bin/bcftools
[02:09:54] Found samtools - /usr/local/bin/samtools
[02:09:54] Found java - /usr/local/bin/java
[02:09:54] Found snpEff - /usr/local/bin/snpEff
[02:09:54] Found samclip - /usr/local/bin/samclip
[02:09:54] Found seqtk - /usr/local/bin/seqtk
[02:09:54] Found parallel - /usr/local/bin/parallel
[02:09:54] Found freebayes - /usr/local/bin/freebayes
[02:09:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:09:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:09:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:09:54] Found vcfuniq - /usr/local/bin/vcfuniq
[02:09:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:09:54] Found gzip - /bin/gzip
[02:09:54] Found vt - /usr/local/bin/vt
[02:09:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:09:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:09:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:09:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:09:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:09:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:09:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:09:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:10:17] This is snippy 4.6.0Show full stderr[02:10:17] This is snippy 4.6.0
[02:10:17] Written by Torsten Seemann
[02:10:17] Obtained from https://github.com/tseemann/snippy
[02:10:17] Detected operating system: linux
[02:10:17] Enabling bundled linux tools.
[02:10:17] Found bwa - /usr/local/bin/bwa
[02:10:17] Found bcftools - /usr/local/bin/bcftools
[02:10:17] Found samtools - /usr/local/bin/samtools
[02:10:17] Found java - /usr/local/bin/java
[02:10:18] Found snpEff - /usr/local/bin/snpEff
[02:10:18] Found samclip - /usr/local/bin/samclip
[02:10:18] Found seqtk - /usr/local/bin/seqtk
[02:10:18] Found parallel - /usr/local/bin/parallel
[02:10:18] Found freebayes - /usr/local/bin/freebayes
[02:10:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:10:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:10:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:10:18] Found vcfuniq - /usr/local/bin/vcfuniq
[02:10:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:10:18] Found gzip - /bin/gzip
[02:10:18] Found vt - /usr/local/bin/vt
[02:10:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:10:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:10:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:10:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:10:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:10:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:10:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:10:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:17:59] This is snippy 4.6.0Show full stderr[02:17:59] This is snippy 4.6.0
[02:17:59] Written by Torsten Seemann
[02:17:59] Obtained from https://github.com/tseemann/snippy
[02:17:59] Detected operating system: linux
[02:17:59] Enabling bundled linux tools.
[02:17:59] Found bwa - /usr/local/bin/bwa
[02:17:59] Found bcftools - /usr/local/bin/bcftools
[02:17:59] Found samtools - /usr/local/bin/samtools
[02:17:59] Found java - /usr/local/bin/java
[02:17:59] Found snpEff - /usr/local/bin/snpEff
[02:17:59] Found samclip - /usr/local/bin/samclip
[02:17:59] Found seqtk - /usr/local/bin/seqtk
[02:17:59] Found parallel - /usr/local/bin/parallel
[02:17:59] Found freebayes - /usr/local/bin/freebayes
[02:17:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:17:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:17:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:17:59] Found vcfuniq - /usr/local/bin/vcfuniq
[02:17:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:17:59] Found gzip - /bin/gzip
[02:17:59] Found vt - /usr/local/bin/vt
[02:17:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:17:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:18:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:18:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:18:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:18:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:18:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:18:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:18:13] This is snippy 4.6.0Show full stderr[02:18:13] This is snippy 4.6.0
[02:18:13] Written by Torsten Seemann
[02:18:13] Obtained from https://github.com/tseemann/snippy
[02:18:13] Detected operating system: linux
[02:18:13] Enabling bundled linux tools.
[02:18:13] Found bwa - /usr/local/bin/bwa
[02:18:13] Found bcftools - /usr/local/bin/bcftools
[02:18:13] Found samtools - /usr/local/bin/samtools
[02:18:13] Found java - /usr/local/bin/java
[02:18:13] Found snpEff - /usr/local/bin/snpEff
[02:18:13] Found samclip - /usr/local/bin/samclip
[02:18:13] Found seqtk - /usr/local/bin/seqtk
[02:18:13] Found parallel - /usr/local/bin/parallel
[02:18:13] Found freebayes - /usr/local/bin/freebayes
[02:18:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:18:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:18:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:18:13] Found vcfuniq - /usr/local/bin/vcfuniq
[02:18:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:18:13] Found gzip - /bin/gzip
[02:18:13] Found vt - /usr/local/bin/vt
[02:18:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:18:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:18:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:18:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:18:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:18:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:18:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:18:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:18:29] This is snippy 4.6.0Show full stderr[02:18:29] This is snippy 4.6.0
[02:18:29] Written by Torsten Seemann
[02:18:29] Obtained from https://github.com/tseemann/snippy
[02:18:29] Detected operating system: linux
[02:18:29] Enabling bundled linux tools.
[02:18:29] Found bwa - /usr/local/bin/bwa
[02:18:29] Found bcftools - /usr/local/bin/bcftools
[02:18:29] Found samtools - /usr/local/bin/samtools
[02:18:29] Found java - /usr/local/bin/java
[02:18:29] Found snpEff - /usr/local/bin/snpEff
[02:18:29] Found samclip - /usr/local/bin/samclip
[02:18:29] Found seqtk - /usr/local/bin/seqtk
[02:18:29] Found parallel - /usr/local/bin/parallel
[02:18:29] Found freebayes - /usr/local/bin/freebayes
[02:18:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:18:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:18:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:18:29] Found vcfuniq - /usr/local/bin/vcfuniq
[02:18:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:18:29] Found gzip - /bin/gzip
[02:18:29] Found vt - /usr/local/bin/vt
[02:18:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:18:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:18:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:18:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:18:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:18:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:18:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:18:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:02:18] This is snippy 4.6.0Show full stderr[23:02:18] This is snippy 4.6.0
[23:02:18] Written by Torsten Seemann
[23:02:18] Obtained from https://github.com/tseemann/snippy
[23:02:18] Detected operating system: linux
[23:02:18] Enabling bundled linux tools.
[23:02:18] Found bwa - /usr/local/bin/bwa
[23:02:18] Found bcftools - /usr/local/bin/bcftools
[23:02:18] Found samtools - /usr/local/bin/samtools
[23:02:18] Found java - /usr/local/bin/java
[23:02:18] Found snpEff - /usr/local/bin/snpEff
[23:02:18] Found samclip - /usr/local/bin/samclip
[23:02:18] Found seqtk - /usr/local/bin/seqtk
[23:02:18] Found parallel - /usr/local/bin/parallel
[23:02:18] Found freebayes - /usr/local/bin/freebayes
[23:02:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:02:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:02:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:02:18] Found vcfuniq - /usr/local/bin/vcfuniq
[23:02:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:02:18] Found gzip - /bin/gzip
[23:02:18] Found vt - /usr/local/bin/vt
[23:02:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:02:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:02:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:02:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:02:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:02:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:02:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:02:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:26:27] This is snippy 4.6.0Show full stderr[23:26:27] This is snippy 4.6.0
[23:26:27] Written by Torsten Seemann
[23:26:27] Obtained from https://github.com/tseemann/snippy
[23:26:27] Detected operating system: linux
[23:26:27] Enabling bundled linux tools.
[23:26:27] Found bwa - /usr/local/bin/bwa
[23:26:27] Found bcftools - /usr/local/bin/bcftools
[23:26:27] Found samtools - /usr/local/bin/samtools
[23:26:27] Found java - /usr/local/bin/java
[23:26:27] Found snpEff - /usr/local/bin/snpEff
[23:26:27] Found samclip - /usr/local/bin/samclip
[23:26:27] Found seqtk - /usr/local/bin/seqtk
[23:26:27] Found parallel - /usr/local/bin/parallel
[23:26:27] Found freebayes - /usr/local/bin/freebayes
[23:26:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:26:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:26:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:26:27] Found vcfuniq - /usr/local/bin/vcfuniq
[23:26:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:26:27] Found gzip - /bin/gzip
[23:26:27] Found vt - /usr/local/bin/vt
[23:26:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:26:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:26:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:26:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:26:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:26:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:26:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:26:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:27:06] This is snippy 4.6.0Show full stderr[23:27:06] This is snippy 4.6.0
[23:27:06] Written by Torsten Seemann
[23:27:06] Obtained from https://github.com/tseemann/snippy
[23:27:06] Detected operating system: linux
[23:27:06] Enabling bundled linux tools.
[23:27:06] Found bwa - /usr/local/bin/bwa
[23:27:06] Found bcftools - /usr/local/bin/bcftools
[23:27:06] Found samtools - /usr/local/bin/samtools
[23:27:06] Found java - /usr/local/bin/java
[23:27:06] Found snpEff - /usr/local/bin/snpEff
[23:27:06] Found samclip - /usr/local/bin/samclip
[23:27:06] Found seqtk - /usr/local/bin/seqtk
[23:27:06] Found parallel - /usr/local/bin/parallel
[23:27:06] Found freebayes - /usr/local/bin/freebayes
[23:27:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:27:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:27:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:27:06] Found vcfuniq - /usr/local/bin/vcfuniq
[23:27:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:27:06] Found gzip - /bin/gzip
[23:27:06] Found vt - /usr/local/bin/vt
[23:27:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:27:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:27:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:27:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:27:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:27:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:27:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:27:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:42:44] This is snippy 4.6.0Show full stderr[23:42:44] This is snippy 4.6.0
[23:42:44] Written by Torsten Seemann
[23:42:44] Obtained from https://github.com/tseemann/snippy
[23:42:44] Detected operating system: linux
[23:42:44] Enabling bundled linux tools.
[23:42:44] Found bwa - /usr/local/bin/bwa
[23:42:44] Found bcftools - /usr/local/bin/bcftools
[23:42:44] Found samtools - /usr/local/bin/samtools
[23:42:44] Found java - /usr/local/bin/java
[23:42:44] Found snpEff - /usr/local/bin/snpEff
[23:42:44] Found samclip - /usr/local/bin/samclip
[23:42:44] Found seqtk - /usr/local/bin/seqtk
[23:42:44] Found parallel - /usr/local/bin/parallel
[23:42:44] Found freebayes - /usr/local/bin/freebayes
[23:42:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:42:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:42:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:42:44] Found vcfuniq - /usr/local/bin/vcfuniq
[23:42:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:42:44] Found gzip - /bin/gzip
[23:42:44] Found vt - /usr/local/bin/vt
[23:42:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:42:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:42:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:42:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:42:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:42:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:42:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:42:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:43:06] This is snippy 4.6.0Show full stderr[23:43:06] This is snippy 4.6.0
[23:43:06] Written by Torsten Seemann
[23:43:06] Obtained from https://github.com/tseemann/snippy
[23:43:06] Detected operating system: linux
[23:43:06] Enabling bundled linux tools.
[23:43:06] Found bwa - /usr/local/bin/bwa
[23:43:06] Found bcftools - /usr/local/bin/bcftools
[23:43:06] Found samtools - /usr/local/bin/samtools
[23:43:06] Found java - /usr/local/bin/java
[23:43:06] Found snpEff - /usr/local/bin/snpEff
[23:43:06] Found samclip - /usr/local/bin/samclip
[23:43:06] Found seqtk - /usr/local/bin/seqtk
[23:43:06] Found parallel - /usr/local/bin/parallel
[23:43:06] Found freebayes - /usr/local/bin/freebayes
[23:43:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:43:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:43:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:43:06] Found vcfuniq - /usr/local/bin/vcfuniq
[23:43:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:43:06] Found gzip - /bin/gzip
[23:43:06] Found vt - /usr/local/bin/vt
[23:43:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:43:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:43:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:43:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:43:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:43:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:43:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:43:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:59:12] This is snippy 4.6.0Show full stderr[23:59:12] This is snippy 4.6.0
[23:59:12] Written by Torsten Seemann
[23:59:12] Obtained from https://github.com/tseemann/snippy
[23:59:12] Detected operating system: linux
[23:59:12] Enabling bundled linux tools.
[23:59:12] Found bwa - /usr/local/bin/bwa
[23:59:12] Found bcftools - /usr/local/bin/bcftools
[23:59:12] Found samtools - /usr/local/bin/samtools
[23:59:12] Found java - /usr/local/bin/java
[23:59:12] Found snpEff - /usr/local/bin/snpEff
[23:59:12] Found samclip - /usr/local/bin/samclip
[23:59:12] Found seqtk - /usr/local/bin/seqtk
[23:59:12] Found parallel - /usr/local/bin/parallel
[23:59:12] Found freebayes - /usr/local/bin/freebayes
[23:59:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:59:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:59:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:59:12] Found vcfuniq - /usr/local/bin/vcfuniq
[23:59:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:59:12] Found gzip - /bin/gzip
[23:59:12] Found vt - /usr/local/bin/vt
[23:59:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:59:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:59:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:59:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:59:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:59:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:59:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:59:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:52:58] This is snippy 4.6.0Show full stderr[17:52:58] This is snippy 4.6.0
[17:52:58] Written by Torsten Seemann
[17:52:58] Obtained from https://github.com/tseemann/snippy
[17:52:58] Detected operating system: linux
[17:52:58] Enabling bundled linux tools.
[17:52:58] Found bwa - /usr/local/bin/bwa
[17:52:58] Found bcftools - /usr/local/bin/bcftools
[17:52:58] Found samtools - /usr/local/bin/samtools
[17:52:58] Found java - /usr/local/bin/java
[17:52:58] Found snpEff - /usr/local/bin/snpEff
[17:52:58] Found samclip - /usr/local/bin/samclip
[17:52:58] Found seqtk - /usr/local/bin/seqtk
[17:52:58] Found parallel - /usr/local/bin/parallel
[17:52:58] Found freebayes - /usr/local/bin/freebayes
[17:52:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:52:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:52:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:52:58] Found vcfuniq - /usr/local/bin/vcfuniq
[17:52:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:52:58] Found gzip - /bin/gzip
[17:52:58] Found vt - /usr/local/bin/vt
[17:52:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:52:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:52:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:52:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:52:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:52:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:52:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:52:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:07:28] This is snippy 4.6.0Show full stderr[00:07:28] This is snippy 4.6.0
[00:07:28] Written by Torsten Seemann
[00:07:28] Obtained from https://github.com/tseemann/snippy
[00:07:28] Detected operating system: linux
[00:07:28] Enabling bundled linux tools.
[00:07:28] Found bwa - /usr/local/bin/bwa
[00:07:28] Found bcftools - /usr/local/bin/bcftools
[00:07:29] Found samtools - /usr/local/bin/samtools
[00:07:29] Found java - /usr/local/bin/java
[00:07:29] Found snpEff - /usr/local/bin/snpEff
[00:07:29] Found samclip - /usr/local/bin/samclip
[00:07:29] Found seqtk - /usr/local/bin/seqtk
[00:07:29] Found parallel - /usr/local/bin/parallel
[00:07:29] Found freebayes - /usr/local/bin/freebayes
[00:07:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:07:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:07:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:07:29] Found vcfuniq - /usr/local/bin/vcfuniq
[00:07:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:07:29] Found gzip - /bin/gzip
[00:07:29] Found vt - /usr/local/bin/vt
[00:07:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:07:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:07:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:07:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:07:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:07:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:07:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:07:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:09:26] This is snippy 4.6.0Show full stderr[18:09:26] This is snippy 4.6.0
[18:09:26] Written by Torsten Seemann
[18:09:26] Obtained from https://github.com/tseemann/snippy
[18:09:26] Detected operating system: linux
[18:09:26] Enabling bundled linux tools.
[18:09:26] Found bwa - /usr/local/bin/bwa
[18:09:26] Found bcftools - /usr/local/bin/bcftools
[18:09:26] Found samtools - /usr/local/bin/samtools
[18:09:26] Found java - /usr/local/bin/java
[18:09:26] Found snpEff - /usr/local/bin/snpEff
[18:09:26] Found samclip - /usr/local/bin/samclip
[18:09:26] Found seqtk - /usr/local/bin/seqtk
[18:09:26] Found parallel - /usr/local/bin/parallel
[18:09:26] Found freebayes - /usr/local/bin/freebayes
[18:09:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:09:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:09:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:09:26] Found vcfuniq - /usr/local/bin/vcfuniq
[18:09:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:09:26] Found gzip - /bin/gzip
[18:09:26] Found vt - /usr/local/bin/vt
[18:09:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:09:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:09:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:09:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:09:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:09:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:09:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:09:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [22:03:19] This is snippy 4.6.0Show full stderr[22:03:19] This is snippy 4.6.0
[22:03:19] Written by Torsten Seemann
[22:03:19] Obtained from https://github.com/tseemann/snippy
[22:03:19] Detected operating system: linux
[22:03:19] Enabling bundled linux tools.
[22:03:19] Found bwa - /usr/local/bin/bwa
[22:03:19] Found bcftools - /usr/local/bin/bcftools
[22:03:19] Found samtools - /usr/local/bin/samtools
[22:03:19] Found java - /usr/local/bin/java
[22:03:19] Found snpEff - /usr/local/bin/snpEff
[22:03:19] Found samclip - /usr/local/bin/samclip
[22:03:19] Found seqtk - /usr/local/bin/seqtk
[22:03:19] Found parallel - /usr/local/bin/parallel
[22:03:19] Found freebayes - /usr/local/bin/freebayes
[22:03:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:03:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:03:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:03:19] Found vcfuniq - /usr/local/bin/vcfuniq
[22:03:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:03:19] Found gzip - /bin/gzip
[22:03:19] Found vt - /usr/local/bin/vt
[22:03:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:03:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:03:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:03:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:03:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:03:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:03:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:03:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:17:06] This is snippy 4.6.0Show full stderr[00:17:06] This is snippy 4.6.0
[00:17:06] Written by Torsten Seemann
[00:17:06] Obtained from https://github.com/tseemann/snippy
[00:17:06] Detected operating system: linux
[00:17:06] Enabling bundled linux tools.
[00:17:06] Found bwa - /usr/local/bin/bwa
[00:17:06] Found bcftools - /usr/local/bin/bcftools
[00:17:06] Found samtools - /usr/local/bin/samtools
[00:17:06] Found java - /usr/local/bin/java
[00:17:06] Found snpEff - /usr/local/bin/snpEff
[00:17:06] Found samclip - /usr/local/bin/samclip
[00:17:06] Found seqtk - /usr/local/bin/seqtk
[00:17:06] Found parallel - /usr/local/bin/parallel
[00:17:06] Found freebayes - /usr/local/bin/freebayes
[00:17:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:17:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:17:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:17:06] Found vcfuniq - /usr/local/bin/vcfuniq
[00:17:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:17:06] Found gzip - /bin/gzip
[00:17:06] Found vt - /usr/local/bin/vt
[00:17:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:17:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:17:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:17:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:17:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:17:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:17:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:17:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:43:37] This is snippy 4.6.0Show full stderr[00:43:37] This is snippy 4.6.0
[00:43:37] Written by Torsten Seemann
[00:43:37] Obtained from https://github.com/tseemann/snippy
[00:43:37] Detected operating system: linux
[00:43:37] Enabling bundled linux tools.
[00:43:37] Found bwa - /usr/local/bin/bwa
[00:43:37] Found bcftools - /usr/local/bin/bcftools
[00:43:37] Found samtools - /usr/local/bin/samtools
[00:43:37] Found java - /usr/local/bin/java
[00:43:37] Found snpEff - /usr/local/bin/snpEff
[00:43:37] Found samclip - /usr/local/bin/samclip
[00:43:37] Found seqtk - /usr/local/bin/seqtk
[00:43:37] Found parallel - /usr/local/bin/parallel
[00:43:37] Found freebayes - /usr/local/bin/freebayes
[00:43:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:43:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:43:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:43:37] Found vcfuniq - /usr/local/bin/vcfuniq
[00:43:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:43:37] Found gzip - /bin/gzip
[00:43:37] Found vt - /usr/local/bin/vt
[00:43:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:43:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:43:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:43:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:43:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:43:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:43:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:43:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:44:33] This is snippy 4.6.0Show full stderr[00:44:33] This is snippy 4.6.0
[00:44:33] Written by Torsten Seemann
[00:44:33] Obtained from https://github.com/tseemann/snippy
[00:44:33] Detected operating system: linux
[00:44:33] Enabling bundled linux tools.
[00:44:33] Found bwa - /usr/local/bin/bwa
[00:44:33] Found bcftools - /usr/local/bin/bcftools
[00:44:33] Found samtools - /usr/local/bin/samtools
[00:44:33] Found java - /usr/local/bin/java
[00:44:33] Found snpEff - /usr/local/bin/snpEff
[00:44:33] Found samclip - /usr/local/bin/samclip
[00:44:33] Found seqtk - /usr/local/bin/seqtk
[00:44:33] Found parallel - /usr/local/bin/parallel
[00:44:33] Found freebayes - /usr/local/bin/freebayes
[00:44:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:44:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:44:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:44:33] Found vcfuniq - /usr/local/bin/vcfuniq
[00:44:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:44:33] Found gzip - /bin/gzip
[00:44:33] Found vt - /usr/local/bin/vt
[00:44:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:44:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:44:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:44:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:44:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:44:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:44:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:44:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:17:27] This is snippy 4.6.0Show full stderr[01:17:27] This is snippy 4.6.0
[01:17:27] Written by Torsten Seemann
[01:17:27] Obtained from https://github.com/tseemann/snippy
[01:17:27] Detected operating system: linux
[01:17:27] Enabling bundled linux tools.
[01:17:27] Found bwa - /usr/local/bin/bwa
[01:17:27] Found bcftools - /usr/local/bin/bcftools
[01:17:27] Found samtools - /usr/local/bin/samtools
[01:17:27] Found java - /usr/local/bin/java
[01:17:27] Found snpEff - /usr/local/bin/snpEff
[01:17:27] Found samclip - /usr/local/bin/samclip
[01:17:27] Found seqtk - /usr/local/bin/seqtk
[01:17:27] Found parallel - /usr/local/bin/parallel
[01:17:27] Found freebayes - /usr/local/bin/freebayes
[01:17:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:17:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:17:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:17:27] Found vcfuniq - /usr/local/bin/vcfuniq
[01:17:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:17:27] Found gzip - /bin/gzip
[01:17:27] Found vt - /usr/local/bin/vt
[01:17:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:17:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:17:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:17:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:17:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:17:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:17:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:17:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:17:55] This is snippy 4.6.0Show full stderr[01:17:55] This is snippy 4.6.0
[01:17:55] Written by Torsten Seemann
[01:17:55] Obtained from https://github.com/tseemann/snippy
[01:17:55] Detected operating system: linux
[01:17:55] Enabling bundled linux tools.
[01:17:55] Found bwa - /usr/local/bin/bwa
[01:17:55] Found bcftools - /usr/local/bin/bcftools
[01:17:55] Found samtools - /usr/local/bin/samtools
[01:17:55] Found java - /usr/local/bin/java
[01:17:55] Found snpEff - /usr/local/bin/snpEff
[01:17:55] Found samclip - /usr/local/bin/samclip
[01:17:55] Found seqtk - /usr/local/bin/seqtk
[01:17:55] Found parallel - /usr/local/bin/parallel
[01:17:55] Found freebayes - /usr/local/bin/freebayes
[01:17:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:17:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:17:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:17:55] Found vcfuniq - /usr/local/bin/vcfuniq
[01:17:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:17:55] Found gzip - /bin/gzip
[01:17:55] Found vt - /usr/local/bin/vt
[01:17:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:17:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:17:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:17:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:17:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:17:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:17:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:17:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:18:36] This is snippy 4.6.0Show full stderr[23:18:36] This is snippy 4.6.0
[23:18:36] Written by Torsten Seemann
[23:18:36] Obtained from https://github.com/tseemann/snippy
[23:18:36] Detected operating system: linux
[23:18:36] Enabling bundled linux tools.
[23:18:36] Found bwa - /usr/local/bin/bwa
[23:18:36] Found bcftools - /usr/local/bin/bcftools
[23:18:36] Found samtools - /usr/local/bin/samtools
[23:18:36] Found java - /usr/local/bin/java
[23:18:36] Found snpEff - /usr/local/bin/snpEff
[23:18:36] Found samclip - /usr/local/bin/samclip
[23:18:36] Found seqtk - /usr/local/bin/seqtk
[23:18:36] Found parallel - /usr/local/bin/parallel
[23:18:36] Found freebayes - /usr/local/bin/freebayes
[23:18:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:18:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:18:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:18:36] Found vcfuniq - /usr/local/bin/vcfuniq
[23:18:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:18:36] Found gzip - /bin/gzip
[23:18:36] Found vt - /usr/local/bin/vt
[23:18:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:18:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:18:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:18:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:18:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:18:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:18:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:18:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:35:06] This is snippy 4.6.0Show full stderr[23:35:06] This is snippy 4.6.0
[23:35:06] Written by Torsten Seemann
[23:35:06] Obtained from https://github.com/tseemann/snippy
[23:35:06] Detected operating system: linux
[23:35:06] Enabling bundled linux tools.
[23:35:06] Found bwa - /usr/local/bin/bwa
[23:35:06] Found bcftools - /usr/local/bin/bcftools
[23:35:06] Found samtools - /usr/local/bin/samtools
[23:35:06] Found java - /usr/local/bin/java
[23:35:06] Found snpEff - /usr/local/bin/snpEff
[23:35:06] Found samclip - /usr/local/bin/samclip
[23:35:06] Found seqtk - /usr/local/bin/seqtk
[23:35:06] Found parallel - /usr/local/bin/parallel
[23:35:06] Found freebayes - /usr/local/bin/freebayes
[23:35:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:35:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:35:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:35:06] Found vcfuniq - /usr/local/bin/vcfuniq
[23:35:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:35:06] Found gzip - /bin/gzip
[23:35:06] Found vt - /usr/local/bin/vt
[23:35:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:35:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:35:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:35:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:35:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:35:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:35:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:35:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:58:42] This is snippy 4.6.0Show full stderr[23:58:42] This is snippy 4.6.0
[23:58:42] Written by Torsten Seemann
[23:58:42] Obtained from https://github.com/tseemann/snippy
[23:58:42] Detected operating system: linux
[23:58:42] Enabling bundled linux tools.
[23:58:42] Found bwa - /usr/local/bin/bwa
[23:58:42] Found bcftools - /usr/local/bin/bcftools
[23:58:42] Found samtools - /usr/local/bin/samtools
[23:58:42] Found java - /usr/local/bin/java
[23:58:42] Found snpEff - /usr/local/bin/snpEff
[23:58:42] Found samclip - /usr/local/bin/samclip
[23:58:42] Found seqtk - /usr/local/bin/seqtk
[23:58:42] Found parallel - /usr/local/bin/parallel
[23:58:42] Found freebayes - /usr/local/bin/freebayes
[23:58:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:58:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:58:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:58:42] Found vcfuniq - /usr/local/bin/vcfuniq
[23:58:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:58:42] Found gzip - /bin/gzip
[23:58:42] Found vt - /usr/local/bin/vt
[23:58:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:58:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:58:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:58:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:58:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:58:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:58:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:58:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [20:30:48] This is snippy 4.6.0Show full stderr[20:30:48] This is snippy 4.6.0
[20:30:48] Written by Torsten Seemann
[20:30:48] Obtained from https://github.com/tseemann/snippy
[20:30:48] Detected operating system: linux
[20:30:48] Enabling bundled linux tools.
[20:30:48] Found bwa - /usr/local/bin/bwa
[20:30:48] Found bcftools - /usr/local/bin/bcftools
[20:30:48] Found samtools - /usr/local/bin/samtools
[20:30:48] Found java - /usr/local/bin/java
[20:30:48] Found snpEff - /usr/local/bin/snpEff
[20:30:48] Found samclip - /usr/local/bin/samclip
[20:30:48] Found seqtk - /usr/local/bin/seqtk
[20:30:48] Found parallel - /usr/local/bin/parallel
[20:30:48] Found freebayes - /usr/local/bin/freebayes
[20:30:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:30:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:30:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:30:48] Found vcfuniq - /usr/local/bin/vcfuniq
[20:30:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:30:48] Found gzip - /bin/gzip
[20:30:48] Found vt - /usr/local/bin/vt
[20:30:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:30:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:30:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:30:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:30:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:30:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:30:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:30:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:59:36] This is snippy 4.6.0Show full stderr[23:59:36] This is snippy 4.6.0
[23:59:36] Written by Torsten Seemann
[23:59:36] Obtained from https://github.com/tseemann/snippy
[23:59:36] Detected operating system: linux
[23:59:36] Enabling bundled linux tools.
[23:59:36] Found bwa - /usr/local/bin/bwa
[23:59:36] Found bcftools - /usr/local/bin/bcftools
[23:59:36] Found samtools - /usr/local/bin/samtools
[23:59:36] Found java - /usr/local/bin/java
[23:59:36] Found snpEff - /usr/local/bin/snpEff
[23:59:36] Found samclip - /usr/local/bin/samclip
[23:59:36] Found seqtk - /usr/local/bin/seqtk
[23:59:36] Found parallel - /usr/local/bin/parallel
[23:59:36] Found freebayes - /usr/local/bin/freebayes
[23:59:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:59:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:59:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:59:36] Found vcfuniq - /usr/local/bin/vcfuniq
[23:59:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:59:36] Found gzip - /bin/gzip
[23:59:36] Found vt - /usr/local/bin/vt
[23:59:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:59:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:59:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:59:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:59:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:59:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:59:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:59:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:43:25] This is snippy 4.6.0Show full stderr[00:43:25] This is snippy 4.6.0
[00:43:25] Written by Torsten Seemann
[00:43:25] Obtained from https://github.com/tseemann/snippy
[00:43:25] Detected operating system: linux
[00:43:25] Enabling bundled linux tools.
[00:43:25] Found bwa - /usr/local/bin/bwa
[00:43:25] Found bcftools - /usr/local/bin/bcftools
[00:43:25] Found samtools - /usr/local/bin/samtools
[00:43:25] Found java - /usr/local/bin/java
[00:43:25] Found snpEff - /usr/local/bin/snpEff
[00:43:25] Found samclip - /usr/local/bin/samclip
[00:43:25] Found seqtk - /usr/local/bin/seqtk
[00:43:25] Found parallel - /usr/local/bin/parallel
[00:43:25] Found freebayes - /usr/local/bin/freebayes
[00:43:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:43:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:43:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:43:25] Found vcfuniq - /usr/local/bin/vcfuniq
[00:43:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:43:25] Found gzip - /bin/gzip
[00:43:25] Found vt - /usr/local/bin/vt
[00:43:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:43:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:43:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:43:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:43:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:43:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:43:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:43:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [09:47:01] This is snippy 4.6.0Show full stderr[09:47:01] This is snippy 4.6.0
[09:47:01] Written by Torsten Seemann
[09:47:01] Obtained from https://github.com/tseemann/snippy
[09:47:01] Detected operating system: linux
[09:47:01] Enabling bundled linux tools.
[09:47:01] Found bwa - /usr/local/bin/bwa
[09:47:01] Found bcftools - /usr/local/bin/bcftools
[09:47:01] Found samtools - /usr/local/bin/samtools
[09:47:01] Found java - /usr/local/bin/java
[09:47:01] Found snpEff - /usr/local/bin/snpEff
[09:47:01] Found samclip - /usr/local/bin/samclip
[09:47:01] Found seqtk - /usr/local/bin/seqtk
[09:47:01] Found parallel - /usr/local/bin/parallel
[09:47:01] Found freebayes - /usr/local/bin/freebayes
[09:47:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:47:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:47:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:47:01] Found vcfuniq - /usr/local/bin/vcfuniq
[09:47:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:47:01] Found gzip - /bin/gzip
[09:47:01] Found vt - /usr/local/bin/vt
[09:47:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:47:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:47:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:47:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:47:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:47:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:47:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:47:02] Using reference: /jetstream2/scratch/main/jobs/72478623/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat
[09:47:02] Treating reference as 'fasta' format.
[09:47:02] Will use 1 CPU cores.
[09:47:02] Using read file: /jetstream2/scratch/main/jobs/72478623/inputs/dataset_63e50c05-a152-4847-9df5-b0c6a4cb45df.dat
[09:47:02] Using read file: /jetstream2/scratch/main/jobs/72478623/inputs/dataset_63e50c05-a152-4847-9df5-b0c6a4cb45df.dat
[09:47:02] Creating folder: HUAS_MG91
[09:47:02] Changing working directory: HUAS_MG91
[09:47:02] Creating reference folder: reference
[09:47:02] Extracting FASTA and GFF from reference.
[09:47:03] Wrote 3 sequences to ref.fa
[09:47:03] Wrote 0 features to ref.gff
[09:47:03] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[09:47:03] Using BAM RG (Read Group) ID: HUAS_MG91
[09:47:03] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:47:03] Running: bwa index reference/ref.fa 2>> snps.log
[09:47:05] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:47:05] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:47:05] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:47:05] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:47:05] Running: bwa mem -Y -M -R '@RG\tID:HUAS_MG91\tSM:HUAS_MG91' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478623/inputs/dataset_63e50c05-a152-4847-9df5-b0c6a4cb45df.dat /jetstream2/scratch/main/jobs/72478623/inputs/dataset_63e50c05-a152-4847-9df5-b0c6a4cb45df.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478623/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478623/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478623/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loadin |
| 1 | [09:48:40] This is snippy 4.6.0Show full stderr[09:48:40] This is snippy 4.6.0
[09:48:40] Written by Torsten Seemann
[09:48:40] Obtained from https://github.com/tseemann/snippy
[09:48:40] Detected operating system: linux
[09:48:40] Enabling bundled linux tools.
[09:48:40] Found bwa - /usr/local/bin/bwa
[09:48:40] Found bcftools - /usr/local/bin/bcftools
[09:48:40] Found samtools - /usr/local/bin/samtools
[09:48:40] Found java - /usr/local/bin/java
[09:48:40] Found snpEff - /usr/local/bin/snpEff
[09:48:40] Found samclip - /usr/local/bin/samclip
[09:48:40] Found seqtk - /usr/local/bin/seqtk
[09:48:40] Found parallel - /usr/local/bin/parallel
[09:48:40] Found freebayes - /usr/local/bin/freebayes
[09:48:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:48:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:48:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:48:40] Found vcfuniq - /usr/local/bin/vcfuniq
[09:48:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:48:40] Found gzip - /bin/gzip
[09:48:40] Found vt - /usr/local/bin/vt
[09:48:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:48:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:48:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:48:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:48:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:48:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:48:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:48:41] Using reference: /jetstream2/scratch/main/jobs/72478624/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat
[09:48:41] Treating reference as 'fasta' format.
[09:48:41] Will use 1 CPU cores.
[09:48:41] Using read file: /jetstream2/scratch/main/jobs/72478624/inputs/dataset_89739e6d-721b-419b-ae5c-67c39031ebc2.dat
[09:48:41] Using read file: /jetstream2/scratch/main/jobs/72478624/inputs/dataset_89739e6d-721b-419b-ae5c-67c39031ebc2.dat
[09:48:41] Creating folder: GIMV4_001
[09:48:41] Changing working directory: GIMV4_001
[09:48:41] Creating reference folder: reference
[09:48:41] Extracting FASTA and GFF from reference.
[09:48:42] Wrote 3 sequences to ref.fa
[09:48:42] Wrote 0 features to ref.gff
[09:48:42] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[09:48:42] Using BAM RG (Read Group) ID: GIMV4_001
[09:48:42] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:48:42] Running: bwa index reference/ref.fa 2>> snps.log
[09:48:44] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:48:44] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:48:44] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:48:44] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:48:44] Running: bwa mem -Y -M -R '@RG\tID:GIMV4_001\tSM:GIMV4_001' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478624/inputs/dataset_89739e6d-721b-419b-ae5c-67c39031ebc2.dat /jetstream2/scratch/main/jobs/72478624/inputs/dataset_89739e6d-721b-419b-ae5c-67c39031ebc2.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478624/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478624/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478624/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loadin |
| 1 | [09:55:29] This is snippy 4.6.0Show full stderr[09:55:29] This is snippy 4.6.0
[09:55:29] Written by Torsten Seemann
[09:55:29] Obtained from https://github.com/tseemann/snippy
[09:55:29] Detected operating system: linux
[09:55:29] Enabling bundled linux tools.
[09:55:29] Found bwa - /usr/local/bin/bwa
[09:55:29] Found bcftools - /usr/local/bin/bcftools
[09:55:29] Found samtools - /usr/local/bin/samtools
[09:55:29] Found java - /usr/local/bin/java
[09:55:29] Found snpEff - /usr/local/bin/snpEff
[09:55:29] Found samclip - /usr/local/bin/samclip
[09:55:29] Found seqtk - /usr/local/bin/seqtk
[09:55:29] Found parallel - /usr/local/bin/parallel
[09:55:29] Found freebayes - /usr/local/bin/freebayes
[09:55:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:55:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:55:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:55:29] Found vcfuniq - /usr/local/bin/vcfuniq
[09:55:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:55:29] Found gzip - /bin/gzip
[09:55:29] Found vt - /usr/local/bin/vt
[09:55:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:55:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:55:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:55:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:55:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:55:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:55:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:55:31] Using reference: /jetstream2/scratch/main/jobs/72478625/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat
[09:55:31] Treating reference as 'fasta' format.
[09:55:31] Will use 1 CPU cores.
[09:55:31] Using read file: /jetstream2/scratch/main/jobs/72478625/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat
[09:55:31] Using read file: /jetstream2/scratch/main/jobs/72478625/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat
[09:55:31] Creating folder: DSM_41954
[09:55:31] Changing working directory: DSM_41954
[09:55:31] Creating reference folder: reference
[09:55:31] Extracting FASTA and GFF from reference.
[09:55:31] Wrote 3 sequences to ref.fa
[09:55:31] Wrote 0 features to ref.gff
[09:55:31] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[09:55:31] Using BAM RG (Read Group) ID: DSM_41954
[09:55:31] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:55:32] Running: bwa index reference/ref.fa 2>> snps.log
[09:55:34] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:55:34] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:55:34] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:55:34] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:55:34] Running: bwa mem -Y -M -R '@RG\tID:DSM_41954\tSM:DSM_41954' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478625/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat /jetstream2/scratch/main/jobs/72478625/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478625/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478625/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478625/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loadin |
| 1 | [10:06:21] This is snippy 4.6.0Show full stderr[10:06:21] This is snippy 4.6.0
[10:06:21] Written by Torsten Seemann
[10:06:21] Obtained from https://github.com/tseemann/snippy
[10:06:21] Detected operating system: linux
[10:06:21] Enabling bundled linux tools.
[10:06:21] Found bwa - /usr/local/bin/bwa
[10:06:21] Found bcftools - /usr/local/bin/bcftools
[10:06:21] Found samtools - /usr/local/bin/samtools
[10:06:21] Found java - /usr/local/bin/java
[10:06:21] Found snpEff - /usr/local/bin/snpEff
[10:06:21] Found samclip - /usr/local/bin/samclip
[10:06:21] Found seqtk - /usr/local/bin/seqtk
[10:06:21] Found parallel - /usr/local/bin/parallel
[10:06:21] Found freebayes - /usr/local/bin/freebayes
[10:06:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:06:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:06:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:06:21] Found vcfuniq - /usr/local/bin/vcfuniq
[10:06:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:06:21] Found gzip - /bin/gzip
[10:06:21] Found vt - /usr/local/bin/vt
[10:06:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:06:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:06:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:06:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:06:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:06:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:06:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:06:22] Using reference: /jetstream2/scratch/main/jobs/72478626/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat
[10:06:22] Treating reference as 'fasta' format.
[10:06:22] Will use 1 CPU cores.
[10:06:22] Using read file: /jetstream2/scratch/main/jobs/72478626/inputs/dataset_ffcdec99-376b-4a14-addb-2ad3776ef7ec.dat
[10:06:22] Using read file: /jetstream2/scratch/main/jobs/72478626/inputs/dataset_ffcdec99-376b-4a14-addb-2ad3776ef7ec.dat
[10:06:22] Creating folder: DSM_41771
[10:06:22] Changing working directory: DSM_41771
[10:06:22] Creating reference folder: reference
[10:06:22] Extracting FASTA and GFF from reference.
[10:06:23] Wrote 3 sequences to ref.fa
[10:06:23] Wrote 0 features to ref.gff
[10:06:23] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[10:06:23] Using BAM RG (Read Group) ID: DSM_41771
[10:06:23] Running: samtools faidx reference/ref.fa 2>> snps.log
[10:06:23] Running: bwa index reference/ref.fa 2>> snps.log
[10:06:26] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[10:06:26] Running: ln -sf reference/ref.fa . 2>> snps.log
[10:06:26] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[10:06:26] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[10:06:26] Running: bwa mem -Y -M -R '@RG\tID:DSM_41771\tSM:DSM_41771' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478626/inputs/dataset_ffcdec99-376b-4a14-addb-2ad3776ef7ec.dat /jetstream2/scratch/main/jobs/72478626/inputs/dataset_ffcdec99-376b-4a14-addb-2ad3776ef7ec.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478626/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478626/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478626/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loadin |
| 1 | [09:38:17] This is snippy 4.6.0Show full stderr[09:38:17] This is snippy 4.6.0
[09:38:17] Written by Torsten Seemann
[09:38:17] Obtained from https://github.com/tseemann/snippy
[09:38:17] Detected operating system: linux
[09:38:17] Enabling bundled linux tools.
[09:38:17] Found bwa - /usr/local/bin/bwa
[09:38:17] Found bcftools - /usr/local/bin/bcftools
[09:38:17] Found samtools - /usr/local/bin/samtools
[09:38:17] Found java - /usr/local/bin/java
[09:38:17] Found snpEff - /usr/local/bin/snpEff
[09:38:17] Found samclip - /usr/local/bin/samclip
[09:38:17] Found seqtk - /usr/local/bin/seqtk
[09:38:17] Found parallel - /usr/local/bin/parallel
[09:38:17] Found freebayes - /usr/local/bin/freebayes
[09:38:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:38:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:38:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:38:18] Found vcfuniq - /usr/local/bin/vcfuniq
[09:38:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:38:18] Found gzip - /bin/gzip
[09:38:18] Found vt - /usr/local/bin/vt
[09:38:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:38:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:38:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:38:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:38:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:38:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:38:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:38:20] Using reference: /jetstream2/scratch/main/jobs/72478632/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat
[09:38:20] Treating reference as 'fasta' format.
[09:38:20] Will use 1 CPU cores.
[09:38:20] Using read file: /jetstream2/scratch/main/jobs/72478632/inputs/dataset_5b72747f-cdbd-401a-9457-c521691ae78d.dat
[09:38:20] Using read file: /jetstream2/scratch/main/jobs/72478632/inputs/dataset_5b72747f-cdbd-401a-9457-c521691ae78d.dat
[09:38:20] Creating folder: BH_MK_02
[09:38:20] Changing working directory: BH_MK_02
[09:38:20] Creating reference folder: reference
[09:38:20] Extracting FASTA and GFF from reference.
[09:38:21] Wrote 3 sequences to ref.fa
[09:38:21] Wrote 0 features to ref.gff
[09:38:21] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[09:38:21] Using BAM RG (Read Group) ID: BH_MK_02
[09:38:21] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:38:21] Running: bwa index reference/ref.fa 2>> snps.log
[09:38:24] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:38:24] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:38:24] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:38:24] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:38:24] Running: bwa mem -Y -M -R '@RG\tID:BH_MK_02\tSM:BH_MK_02' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478632/inputs/dataset_5b72747f-cdbd-401a-9457-c521691ae78d.dat /jetstream2/scratch/main/jobs/72478632/inputs/dataset_5b72747f-cdbd-401a-9457-c521691ae78d.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478632/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478632/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478632/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: r |
| 1 | [09:46:02] This is snippy 4.6.0Show full stderr[09:46:02] This is snippy 4.6.0
[09:46:02] Written by Torsten Seemann
[09:46:02] Obtained from https://github.com/tseemann/snippy
[09:46:02] Detected operating system: linux
[09:46:02] Enabling bundled linux tools.
[09:46:02] Found bwa - /usr/local/bin/bwa
[09:46:02] Found bcftools - /usr/local/bin/bcftools
[09:46:02] Found samtools - /usr/local/bin/samtools
[09:46:02] Found java - /usr/local/bin/java
[09:46:02] Found snpEff - /usr/local/bin/snpEff
[09:46:02] Found samclip - /usr/local/bin/samclip
[09:46:02] Found seqtk - /usr/local/bin/seqtk
[09:46:02] Found parallel - /usr/local/bin/parallel
[09:46:02] Found freebayes - /usr/local/bin/freebayes
[09:46:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:46:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:46:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:46:02] Found vcfuniq - /usr/local/bin/vcfuniq
[09:46:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:46:02] Found gzip - /bin/gzip
[09:46:02] Found vt - /usr/local/bin/vt
[09:46:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:46:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:46:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:46:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:46:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:46:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:46:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:46:06] Using reference: /jetstream2/scratch/main/jobs/72478636/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat
[09:46:06] Treating reference as 'fasta' format.
[09:46:06] Will use 1 CPU cores.
[09:46:06] Using read file: /jetstream2/scratch/main/jobs/72478636/inputs/dataset_fa7f794c-ea76-43bb-8571-98ff1b98be6f.dat
[09:46:06] Using read file: /jetstream2/scratch/main/jobs/72478636/inputs/dataset_fa7f794c-ea76-43bb-8571-98ff1b98be6f.dat
[09:46:06] Creating folder: ATCC_14922
[09:46:06] Changing working directory: ATCC_14922
[09:46:06] Creating reference folder: reference
[09:46:06] Extracting FASTA and GFF from reference.
[09:46:07] Wrote 3 sequences to ref.fa
[09:46:07] Wrote 0 features to ref.gff
[09:46:07] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[09:46:07] Using BAM RG (Read Group) ID: ATCC_14922
[09:46:07] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:46:07] Running: bwa index reference/ref.fa 2>> snps.log
[09:46:10] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:46:10] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:46:10] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:46:10] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:46:10] Running: bwa mem -Y -M -R '@RG\tID:ATCC_14922\tSM:ATCC_14922' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478636/inputs/dataset_fa7f794c-ea76-43bb-8571-98ff1b98be6f.dat /jetstream2/scratch/main/jobs/72478636/inputs/dataset_fa7f794c-ea76-43bb-8571-98ff1b98be6f.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478636/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478636/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478636/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] L |
| 1 | [10:00:06] This is snippy 4.6.0Show full stderr[10:00:06] This is snippy 4.6.0
[10:00:06] Written by Torsten Seemann
[10:00:06] Obtained from https://github.com/tseemann/snippy
[10:00:06] Detected operating system: linux
[10:00:06] Enabling bundled linux tools.
[10:00:06] Found bwa - /usr/local/bin/bwa
[10:00:06] Found bcftools - /usr/local/bin/bcftools
[10:00:06] Found samtools - /usr/local/bin/samtools
[10:00:06] Found java - /usr/local/bin/java
[10:00:06] Found snpEff - /usr/local/bin/snpEff
[10:00:06] Found samclip - /usr/local/bin/samclip
[10:00:06] Found seqtk - /usr/local/bin/seqtk
[10:00:06] Found parallel - /usr/local/bin/parallel
[10:00:06] Found freebayes - /usr/local/bin/freebayes
[10:00:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:00:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:00:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:00:06] Found vcfuniq - /usr/local/bin/vcfuniq
[10:00:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:00:06] Found gzip - /bin/gzip
[10:00:06] Found vt - /usr/local/bin/vt
[10:00:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:00:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:00:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:00:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:00:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:00:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:00:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:00:07] Using reference: /jetstream2/scratch/main/jobs/72478640/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat
[10:00:07] Treating reference as 'fasta' format.
[10:00:07] Will use 1 CPU cores.
[10:00:07] Using read file: /jetstream2/scratch/main/jobs/72478640/inputs/dataset_bd15df9e-663f-4f70-bb5f-fef1ca7d60f1.dat
[10:00:07] Using read file: /jetstream2/scratch/main/jobs/72478640/inputs/dataset_bd15df9e-663f-4f70-bb5f-fef1ca7d60f1.dat
[10:00:07] Creating folder: 452
[10:00:07] Changing working directory: 452
[10:00:07] Creating reference folder: reference
[10:00:07] Extracting FASTA and GFF from reference.
[10:00:08] Wrote 3 sequences to ref.fa
[10:00:08] Wrote 0 features to ref.gff
[10:00:08] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[10:00:08] Using BAM RG (Read Group) ID: 452
[10:00:08] Running: samtools faidx reference/ref.fa 2>> snps.log
[10:00:08] Running: bwa index reference/ref.fa 2>> snps.log
[10:00:11] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[10:00:11] Running: ln -sf reference/ref.fa . 2>> snps.log
[10:00:11] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[10:00:11] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[10:00:11] Running: bwa mem -Y -M -R '@RG\tID:452\tSM:452' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478640/inputs/dataset_bd15df9e-663f-4f70-bb5f-fef1ca7d60f1.dat /jetstream2/scratch/main/jobs/72478640/inputs/dataset_bd15df9e-663f-4f70-bb5f-fef1ca7d60f1.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478640/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478640/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478640/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samc |
| 1 | [10:00:17] This is snippy 4.6.0Show full stderr[10:00:17] This is snippy 4.6.0
[10:00:17] Written by Torsten Seemann
[10:00:17] Obtained from https://github.com/tseemann/snippy
[10:00:17] Detected operating system: linux
[10:00:17] Enabling bundled linux tools.
[10:00:17] Found bwa - /usr/local/bin/bwa
[10:00:17] Found bcftools - /usr/local/bin/bcftools
[10:00:17] Found samtools - /usr/local/bin/samtools
[10:00:17] Found java - /usr/local/bin/java
[10:00:17] Found snpEff - /usr/local/bin/snpEff
[10:00:17] Found samclip - /usr/local/bin/samclip
[10:00:17] Found seqtk - /usr/local/bin/seqtk
[10:00:17] Found parallel - /usr/local/bin/parallel
[10:00:17] Found freebayes - /usr/local/bin/freebayes
[10:00:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:00:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:00:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:00:17] Found vcfuniq - /usr/local/bin/vcfuniq
[10:00:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:00:17] Found gzip - /bin/gzip
[10:00:18] Found vt - /usr/local/bin/vt
[10:00:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:00:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:00:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:00:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:00:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:00:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:00:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:00:18] Using reference: /jetstream2/scratch/main/jobs/72479039/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat
[10:00:18] Treating reference as 'fasta' format.
[10:00:18] Will use 1 CPU cores.
[10:00:18] Using read file: /jetstream2/scratch/main/jobs/72479039/inputs/dataset_918fb325-2c7e-4099-8f14-75c5948d1f0c.dat
[10:00:18] Using read file: /jetstream2/scratch/main/jobs/72479039/inputs/dataset_918fb325-2c7e-4099-8f14-75c5948d1f0c.dat
[10:00:18] Creating folder: Kala_fna
[10:00:18] Changing working directory: Kala_fna
[10:00:18] Creating reference folder: reference
[10:00:18] Extracting FASTA and GFF from reference.
[10:00:19] Wrote 3 sequences to ref.fa
[10:00:19] Wrote 0 features to ref.gff
[10:00:19] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[10:00:19] Using BAM RG (Read Group) ID: Kala_fna
[10:00:19] Running: samtools faidx reference/ref.fa 2>> snps.log
[10:00:19] Running: bwa index reference/ref.fa 2>> snps.log
[10:00:22] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[10:00:22] Running: ln -sf reference/ref.fa . 2>> snps.log
[10:00:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[10:00:22] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[10:00:22] Running: bwa mem -Y -M -R '@RG\tID:Kala_fna\tSM:Kala_fna' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72479039/inputs/dataset_918fb325-2c7e-4099-8f14-75c5948d1f0c.dat /jetstream2/scratch/main/jobs/72479039/inputs/dataset_918fb325-2c7e-4099-8f14-75c5948d1f0c.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72479039/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72479039/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72479039/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[M::bwa_idx_load_from_disk] re |
| 1 | [10:03:31] This is snippy 4.6.0Show full stderr[10:03:31] This is snippy 4.6.0
[10:03:31] Written by Torsten Seemann
[10:03:31] Obtained from https://github.com/tseemann/snippy
[10:03:31] Detected operating system: linux
[10:03:31] Enabling bundled linux tools.
[10:03:31] Found bwa - /usr/local/bin/bwa
[10:03:31] Found bcftools - /usr/local/bin/bcftools
[10:03:31] Found samtools - /usr/local/bin/samtools
[10:03:31] Found java - /usr/local/bin/java
[10:03:31] Found snpEff - /usr/local/bin/snpEff
[10:03:31] Found samclip - /usr/local/bin/samclip
[10:03:31] Found seqtk - /usr/local/bin/seqtk
[10:03:31] Found parallel - /usr/local/bin/parallel
[10:03:31] Found freebayes - /usr/local/bin/freebayes
[10:03:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:03:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:03:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:03:31] Found vcfuniq - /usr/local/bin/vcfuniq
[10:03:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:03:31] Found gzip - /bin/gzip
[10:03:31] Found vt - /usr/local/bin/vt
[10:03:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:03:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:03:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:03:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:03:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:03:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:03:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:03:35] Using reference: /jetstream2/scratch/main/jobs/72479043/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat
[10:03:35] Treating reference as 'fasta' format.
[10:03:35] Will use 1 CPU cores.
[10:03:35] Using read file: /jetstream2/scratch/main/jobs/72479043/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat
[10:03:35] Using read file: /jetstream2/scratch/main/jobs/72479043/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat
[10:03:35] Creating folder: DSM_41954_fna
[10:03:35] Changing working directory: DSM_41954_fna
[10:03:35] Creating reference folder: reference
[10:03:35] Extracting FASTA and GFF from reference.
[10:03:35] Wrote 3 sequences to ref.fa
[10:03:35] Wrote 0 features to ref.gff
[10:03:35] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time.
[10:03:35] Using BAM RG (Read Group) ID: DSM_41954_fna
[10:03:35] Running: samtools faidx reference/ref.fa 2>> snps.log
[10:03:35] Running: bwa index reference/ref.fa 2>> snps.log
[10:03:38] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[10:03:38] Running: ln -sf reference/ref.fa . 2>> snps.log
[10:03:38] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[10:03:38] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[10:03:38] Running: bwa mem -Y -M -R '@RG\tID:DSM_41954_fna\tSM:DSM_41954_fna' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72479043/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat /jetstream2/scratch/main/jobs/72479043/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72479043/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72479043/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72479043/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseeman |
| 1 | [13:13:52] This is snippy 4.6.0Show full stderr[13:13:52] This is snippy 4.6.0
[13:13:52] Written by Torsten Seemann
[13:13:52] Obtained from https://github.com/tseemann/snippy
[13:13:52] Detected operating system: linux
[13:13:52] Enabling bundled linux tools.
[13:13:52] Found bwa - /usr/local/bin/bwa
[13:13:52] Found bcftools - /usr/local/bin/bcftools
[13:13:52] Found samtools - /usr/local/bin/samtools
[13:13:52] Found java - /usr/local/bin/java
[13:13:52] Found snpEff - /usr/local/bin/snpEff
[13:13:52] Found samclip - /usr/local/bin/samclip
[13:13:52] Found seqtk - /usr/local/bin/seqtk
[13:13:52] Found parallel - /usr/local/bin/parallel
[13:13:52] Found freebayes - /usr/local/bin/freebayes
[13:13:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:13:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:13:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:13:52] Found vcfuniq - /usr/local/bin/vcfuniq
[13:13:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:13:52] Found gzip - /bin/gzip
[13:13:52] Found vt - /usr/local/bin/vt
[13:13:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:13:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:13:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:13:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:13:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:13:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:13:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:13:55] Using reference: /cvmfs/data.galaxyproject.org/byhand/hg38/seq/hg38full.fa
[13:15:20] Treating reference as 'fasta' format.
[13:15:20] Will use 1 CPU cores.
[13:15:20] Using read file: /jetstream2/scratch/main/jobs/72614466/inputs/dataset_f965950b-ce9d-4e63-9a8c-09375be2a2a7.dat
[13:15:20] Using read file: /jetstream2/scratch/main/jobs/72614466/inputs/dataset_f965950b-ce9d-4e63-9a8c-09375be2a2a7.dat
[13:15:20] Creating folder: Y08757_1_fasta
[13:15:20] Changing working directory: Y08757_1_fasta
[13:15:20] Creating reference folder: reference
[13:15:20] Extracting FASTA and GFF from reference.
/jetstream2/scratch/main/jobs/72614466/tool_script.sh: line 23: 21 Killed snippy --outdir 'Y08757_1_fasta' --cpus ${GALAXY_SLOTS:-1} --ram $((${GALAXY_MEMORY_MB:-4096}/1024)) --ref 'ref.fna' --mapqual 60 --mincov 10 --minfrac 0.9 --minqual 100.0 --R1 '/jetstream2/scratch/main/jobs/72614466/inputs/dataset_f965950b-ce9d-4e63-9a8c-09375be2a2a7.dat' --R2 '/jetstream2/scratch/main/jobs/72614466/inputs/dataset_f965950b-ce9d-4e63-9a8c-09375be2a2a7.dat' |
| 1 | [21:30:23] This is snippy 4.6.0Show full stderr[21:30:23] This is snippy 4.6.0
[21:30:23] Written by Torsten Seemann
[21:30:23] Obtained from https://github.com/tseemann/snippy
[21:30:23] Detected operating system: linux
[21:30:23] Enabling bundled linux tools.
[21:30:23] Found bwa - /usr/local/bin/bwa
[21:30:23] Found bcftools - /usr/local/bin/bcftools
[21:30:23] Found samtools - /usr/local/bin/samtools
[21:30:23] Found java - /usr/local/bin/java
[21:30:23] Found snpEff - /usr/local/bin/snpEff
[21:30:23] Found samclip - /usr/local/bin/samclip
[21:30:23] Found seqtk - /usr/local/bin/seqtk
[21:30:23] Found parallel - /usr/local/bin/parallel
[21:30:23] Found freebayes - /usr/local/bin/freebayes
[21:30:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:30:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:30:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:30:23] Found vcfuniq - /usr/local/bin/vcfuniq
[21:30:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:30:23] Found gzip - /bin/gzip
[21:30:23] Found vt - /usr/local/bin/vt
[21:30:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:30:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:30:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:30:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:30:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:30:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:30:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:30:24] Using reference: /corral4/main/objects/5/f/4/dataset_5f437c74-8e7d-4bb3-aa2d-514661d00074.dat
[21:30:24] Treating reference as 'fasta' format.
[21:30:24] Will use 1 CPU cores.
[21:30:24] Using read file: /corral4/main/objects/5/e/8/dataset_5e802efb-d0bd-4b12-98e8-61f6df0fa797.dat
[21:30:24] Creating folder: rpsJ_protein_21_563_fasta
[21:30:24] Changing working directory: rpsJ_protein_21_563_fasta
[21:30:24] Creating reference folder: reference
[21:30:24] Extracting FASTA and GFF from reference.
[21:30:25] Wrote 1 sequences to ref.fa
[21:30:25] Wrote 0 features to ref.gff
[21:30:25] Shredding /corral4/main/objects/5/e/8/dataset_5e802efb-d0bd-4b12-98e8-61f6df0fa797.dat into pseudo-reads
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Sequence is a protein. Cannot revcom.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/lib/site_perl/5.26.2/Bio/Root/Root.pm:447
STACK: Bio::PrimarySeqI::_revcom_from_string /usr/local/lib/site_perl/5.26.2/Bio/PrimarySeqI.pm:401
STACK: Bio::PrimarySeqI::revcom /usr/local/lib/site_perl/5.26.2/Bio/PrimarySeqI.pm:391
STACK: /usr/local/bin/snippy:256
----------------------------------------------------------- |
| 1 | [21:31:33] This is snippy 4.6.0Show full stderr[21:31:33] This is snippy 4.6.0
[21:31:33] Written by Torsten Seemann
[21:31:33] Obtained from https://github.com/tseemann/snippy
[21:31:33] Detected operating system: linux
[21:31:33] Enabling bundled linux tools.
[21:31:33] Found bwa - /usr/local/bin/bwa
[21:31:33] Found bcftools - /usr/local/bin/bcftools
[21:31:33] Found samtools - /usr/local/bin/samtools
[21:31:33] Found java - /usr/local/bin/java
[21:31:33] Found snpEff - /usr/local/bin/snpEff
[21:31:33] Found samclip - /usr/local/bin/samclip
[21:31:33] Found seqtk - /usr/local/bin/seqtk
[21:31:33] Found parallel - /usr/local/bin/parallel
[21:31:33] Found freebayes - /usr/local/bin/freebayes
[21:31:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:31:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:31:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:31:33] Found vcfuniq - /usr/local/bin/vcfuniq
[21:31:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:31:33] Found gzip - /bin/gzip
[21:31:33] Found vt - /usr/local/bin/vt
[21:31:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:31:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:31:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:31:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:31:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:31:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:31:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:31:34] Using reference: /corral4/main/objects/5/f/4/dataset_5f437c74-8e7d-4bb3-aa2d-514661d00074.dat
[21:31:34] Treating reference as 'fasta' format.
[21:31:34] Will use 1 CPU cores.
[21:31:34] Using read file: /corral4/main/objects/5/f/4/dataset_5f437c74-8e7d-4bb3-aa2d-514661d00074.dat
[21:31:34] Creating folder: rpsJ_wt_fasta
[21:31:34] Changing working directory: rpsJ_wt_fasta
[21:31:34] Creating reference folder: reference
[21:31:34] Extracting FASTA and GFF from reference.
[21:31:34] Wrote 1 sequences to ref.fa
[21:31:34] Wrote 0 features to ref.gff
[21:31:34] Shredding /corral4/main/objects/5/f/4/dataset_5f437c74-8e7d-4bb3-aa2d-514661d00074.dat into pseudo-reads
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Sequence is a protein. Cannot revcom.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/lib/site_perl/5.26.2/Bio/Root/Root.pm:447
STACK: Bio::PrimarySeqI::_revcom_from_string /usr/local/lib/site_perl/5.26.2/Bio/PrimarySeqI.pm:401
STACK: Bio::PrimarySeqI::revcom /usr/local/lib/site_perl/5.26.2/Bio/PrimarySeqI.pm:391
STACK: /usr/local/bin/snippy:256
----------------------------------------------------------- |
| 1 | [15:43:45] This is snippy 4.6.0Show full stderr[15:43:45] This is snippy 4.6.0
[15:43:45] Written by Torsten Seemann
[15:43:45] Obtained from https://github.com/tseemann/snippy
[15:43:45] Detected operating system: linux
[15:43:45] Enabling bundled linux tools.
[15:43:45] Found bwa - /usr/local/bin/bwa
[15:43:45] Found bcftools - /usr/local/bin/bcftools
[15:43:45] Found samtools - /usr/local/bin/samtools
[15:43:45] Found java - /usr/local/bin/java
[15:43:45] Found snpEff - /usr/local/bin/snpEff
[15:43:45] Found samclip - /usr/local/bin/samclip
[15:43:45] Found seqtk - /usr/local/bin/seqtk
[15:43:45] Found parallel - /usr/local/bin/parallel
[15:43:45] Found freebayes - /usr/local/bin/freebayes
[15:43:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:43:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:43:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:43:45] Found vcfuniq - /usr/local/bin/vcfuniq
[15:43:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:43:45] Found gzip - /bin/gzip
[15:43:45] Found vt - /usr/local/bin/vt
[15:43:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:43:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:43:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:43:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:43:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:43:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:43:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:43:49] Using reference: /jetstream2/scratch/main/jobs/72674863/inputs/dataset_ce41989f-7ee4-48c8-9529-f279bb8181e6.dat
[15:43:49] Treating reference as 'fasta' format.
[15:43:49] Will use 1 CPU cores.
[15:43:49] Using read file: /jetstream2/scratch/main/jobs/72674863/inputs/dataset_e175473e-d18c-4c53-954e-2fbfddf8326f.dat
[15:43:49] Using read file: /jetstream2/scratch/main/jobs/72674863/inputs/dataset_541c8783-b1da-4b37-b474-654565758f67.dat
[15:43:49] Creating folder: X223RR_5_MIC_C_5_illumina_R1_fastq
[15:43:49] Changing working directory: X223RR_5_MIC_C_5_illumina_R1_fastq
[15:43:49] Creating reference folder: reference
[15:43:49] Extracting FASTA and GFF from reference.
[15:43:49] Wrote 1 sequences to ref.fa
[15:43:49] Wrote 0 features to ref.gff
[15:43:49] Freebayes will process 1 chunks of 5124326 bp, 1 chunks at a time.
[15:43:49] Using BAM RG (Read Group) ID: X223RR_5_MIC_C_5_illumina_R1_fastq
[15:43:49] Running: samtools faidx reference/ref.fa 2>> snps.log
[15:43:49] Running: bwa index reference/ref.fa 2>> snps.log
[15:43:51] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[15:43:51] Running: ln -sf reference/ref.fa . 2>> snps.log
[15:43:51] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[15:43:51] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[15:43:51] Running: bwa mem -Y -M -R '@RG\tID:X223RR_5_MIC_C_5_illumina_R1_fastq\tSM:X223RR_5_MIC_C_5_illumina_R1_fastq' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72674863/inputs/dataset_e175473e-d18c-4c53-954e-2fbfddf8326f.dat /jetstream2/scratch/main/jobs/72674863/inputs/dataset_541c8783-b1da-4b37-b474-654565758f67.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72674863/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72674863/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72674863/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_id |
| 1 | [13:10:54] This is snippy 4.6.0Show full stderr[13:10:54] This is snippy 4.6.0
[13:10:54] Written by Torsten Seemann
[13:10:54] Obtained from https://github.com/tseemann/snippy
[13:10:54] Detected operating system: linux
[13:10:54] Enabling bundled linux tools.
[13:10:54] Found bwa - /usr/local/bin/bwa
[13:10:54] Found bcftools - /usr/local/bin/bcftools
[13:10:54] Found samtools - /usr/local/bin/samtools
[13:10:54] Found java - /usr/local/bin/java
[13:10:54] Found snpEff - /usr/local/bin/snpEff
[13:10:55] Found samclip - /usr/local/bin/samclip
[13:10:55] Found seqtk - /usr/local/bin/seqtk
[13:10:55] Found parallel - /usr/local/bin/parallel
[13:10:55] Found freebayes - /usr/local/bin/freebayes
[13:10:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[13:10:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[13:10:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[13:10:55] Found vcfuniq - /usr/local/bin/vcfuniq
[13:10:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[13:10:55] Found gzip - /bin/gzip
[13:10:55] Found vt - /usr/local/bin/vt
[13:10:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[13:10:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[13:10:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[13:10:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[13:10:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[13:10:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[13:10:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[13:10:55] Using reference: /corral4/main/objects/a/0/8/dataset_a08f00da-ba11-4ad8-99bd-2ff73d9144b8.dat
[13:10:55] Treating reference as 'fasta' format.
[13:10:55] Will use 1 CPU cores.
[13:10:55] Using read file: /corral4/main/objects/3/f/c/dataset_3fc3c6fb-4b76-4b9f-9a2a-95a15be11d61.dat
[13:10:55] Creating folder: Fa_summary_fasta
[13:10:55] Changing working directory: Fa_summary_fasta
[13:10:55] Creating reference folder: reference
[13:10:55] Extracting FASTA and GFF from reference.
[13:10:56] Duplicate sequence FJ445428|2007|SriLanka in /corral4/main/objects/a/0/8/dataset_a08f00da-ba11-4ad8-99bd-2ff73d9144b8.dat |
| 1 | [14:16:52] This is snippy 4.6.0Show full stderr[14:16:52] This is snippy 4.6.0
[14:16:52] Written by Torsten Seemann
[14:16:52] Obtained from https://github.com/tseemann/snippy
[14:16:52] Detected operating system: linux
[14:16:52] Enabling bundled linux tools.
[14:16:52] Found bwa - /usr/local/bin/bwa
[14:16:52] Found bcftools - /usr/local/bin/bcftools
[14:16:52] Found samtools - /usr/local/bin/samtools
[14:16:52] Found java - /usr/local/bin/java
[14:16:52] Found snpEff - /usr/local/bin/snpEff
[14:16:52] Found samclip - /usr/local/bin/samclip
[14:16:52] Found seqtk - /usr/local/bin/seqtk
[14:16:52] Found parallel - /usr/local/bin/parallel
[14:16:52] Found freebayes - /usr/local/bin/freebayes
[14:16:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:16:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:16:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:16:52] Found vcfuniq - /usr/local/bin/vcfuniq
[14:16:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:16:52] Found gzip - /bin/gzip
[14:16:52] Found vt - /usr/local/bin/vt
[14:16:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:16:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:16:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:16:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:16:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:16:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:16:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:16:53] Using reference: /corral4/main/objects/5/3/9/dataset_53992c10-f3f2-4370-8224-5403dd9cd3ea.dat
[14:16:53] Treating reference as 'fasta' format.
[14:16:53] Will use 1 CPU cores.
[14:16:53] Using read file: /corral4/main/objects/1/7/c/dataset_17c5fbb2-e82f-4df4-805c-6028b009d325.dat
[14:16:53] Creating folder: Fa_summary_fasta
[14:16:53] Changing working directory: Fa_summary_fasta
[14:16:53] Creating reference folder: reference
[14:16:53] Extracting FASTA and GFF from reference.
[14:16:54] Wrote 126 sequences to ref.fa
[14:16:54] Wrote 0 features to ref.gff
[14:16:54] Shredding /corral4/main/objects/1/7/c/dataset_17c5fbb2-e82f-4df4-805c-6028b009d325.dat into pseudo-reads
[14:16:57] Wrote 268202 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[14:16:57] Freebayes will process 1 chunks of 1394678 bp, 1 chunks at a time.
[14:16:57] Using BAM RG (Read Group) ID: Fa_summary_fasta
[14:16:57] Running: samtools faidx reference/ref.fa 2>> snps.log
[14:16:57] Running: bwa index reference/ref.fa 2>> snps.log
[14:16:58] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[14:16:58] Running: ln -sf reference/ref.fa . 2>> snps.log
[14:16:58] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[14:16:58] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[14:16:58] Running: bwa mem -Y -M -R '@RG\tID:Fa_summary_fasta\tSM:Fa_summary_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/752/72752915/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/752/72752915/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/752/72752915/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 126 sequences in reference/ref.fa.fai
[M::process] read 4 |
| 1 | [18:43:45] This is snippy 4.6.0Show full stderr[18:43:45] This is snippy 4.6.0
[18:43:45] Written by Torsten Seemann
[18:43:45] Obtained from https://github.com/tseemann/snippy
[18:43:45] Detected operating system: linux
[18:43:45] Enabling bundled linux tools.
[18:43:45] Found bwa - /usr/local/bin/bwa
[18:43:45] Found bcftools - /usr/local/bin/bcftools
[18:43:45] Found samtools - /usr/local/bin/samtools
[18:43:45] Found java - /usr/local/bin/java
[18:43:45] Found snpEff - /usr/local/bin/snpEff
[18:43:45] Found samclip - /usr/local/bin/samclip
[18:43:45] Found seqtk - /usr/local/bin/seqtk
[18:43:45] Found parallel - /usr/local/bin/parallel
[18:43:45] Found freebayes - /usr/local/bin/freebayes
[18:43:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:43:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:43:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:43:45] Found vcfuniq - /usr/local/bin/vcfuniq
[18:43:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:43:45] Found gzip - /bin/gzip
[18:43:45] Found vt - /usr/local/bin/vt
[18:43:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:43:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:43:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:43:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:43:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:43:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:43:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:43:46] Using reference: /corral4/main/objects/d/7/6/dataset_d764c547-d517-4ce6-9e7c-25fb605e00f7.dat
[18:43:46] Treating reference as 'genbank' format.
[18:43:46] Will use 1 CPU cores.
[18:43:46] Using read file: /corral4/main/objects/6/d/e/dataset_6de27930-ce42-4d00-bbc5-7c14263ab5b4.dat
[18:43:46] Using read file: /corral4/main/objects/d/1/6/dataset_d16fac68-6b73-4781-86e3-48a6c0ad4fca.dat
[18:43:46] Creating folder: 172_S96_L001_R1_001_fastq_gz
[18:43:46] Changing working directory: 172_S96_L001_R1_001_fastq_gz
[18:43:46] Creating reference folder: reference
[18:43:46] Extracting FASTA and GFF from reference.
Use of uninitialized value in uc at /usr/local/bin/snippy line 206, <GEN0> line 89.
[18:43:46] Wrote 1 sequences to ref.fa
[18:43:46] Wrote 0 features to ref.gff
[18:43:46] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[18:43:46] Using BAM RG (Read Group) ID: 172_S96_L001_R1_001_fastq_gz
[18:43:46] Running: samtools faidx reference/ref.fa 2>> snps.log
[18:43:46] Error running command, check 172_S96_L001_R1_001_fastq_gz/snps.log |
| 1 | [17:23:57] This is snippy 4.6.0Show full stderr[17:23:57] This is snippy 4.6.0
[17:23:57] Written by Torsten Seemann
[17:23:57] Obtained from https://github.com/tseemann/snippy
[17:23:57] Detected operating system: linux
[17:23:57] Enabling bundled linux tools.
[17:23:57] Found bwa - /usr/local/bin/bwa
[17:23:57] Found bcftools - /usr/local/bin/bcftools
[17:23:57] Found samtools - /usr/local/bin/samtools
[17:23:57] Found java - /usr/local/bin/java
[17:23:57] Found snpEff - /usr/local/bin/snpEff
[17:23:58] Found samclip - /usr/local/bin/samclip
[17:23:58] Found seqtk - /usr/local/bin/seqtk
[17:23:58] Found parallel - /usr/local/bin/parallel
[17:23:58] Found freebayes - /usr/local/bin/freebayes
[17:23:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:23:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:23:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:23:58] Found vcfuniq - /usr/local/bin/vcfuniq
[17:23:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:23:58] Found gzip - /bin/gzip
[17:23:58] Found vt - /usr/local/bin/vt
[17:23:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:23:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:23:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:23:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:23:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:23:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:23:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:23:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:02] This is snippy 4.6.0Show full stderr[17:24:02] This is snippy 4.6.0
[17:24:02] Written by Torsten Seemann
[17:24:02] Obtained from https://github.com/tseemann/snippy
[17:24:02] Detected operating system: linux
[17:24:02] Enabling bundled linux tools.
[17:24:02] Found bwa - /usr/local/bin/bwa
[17:24:02] Found bcftools - /usr/local/bin/bcftools
[17:24:02] Found samtools - /usr/local/bin/samtools
[17:24:02] Found java - /usr/local/bin/java
[17:24:02] Found snpEff - /usr/local/bin/snpEff
[17:24:02] Found samclip - /usr/local/bin/samclip
[17:24:02] Found seqtk - /usr/local/bin/seqtk
[17:24:02] Found parallel - /usr/local/bin/parallel
[17:24:02] Found freebayes - /usr/local/bin/freebayes
[17:24:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:02] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:02] Found gzip - /bin/gzip
[17:24:02] Found vt - /usr/local/bin/vt
[17:24:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:15] This is snippy 4.6.0Show full stderr[17:24:15] This is snippy 4.6.0
[17:24:15] Written by Torsten Seemann
[17:24:15] Obtained from https://github.com/tseemann/snippy
[17:24:15] Detected operating system: linux
[17:24:15] Enabling bundled linux tools.
[17:24:15] Found bwa - /usr/local/bin/bwa
[17:24:15] Found bcftools - /usr/local/bin/bcftools
[17:24:15] Found samtools - /usr/local/bin/samtools
[17:24:15] Found java - /usr/local/bin/java
[17:24:15] Found snpEff - /usr/local/bin/snpEff
[17:24:15] Found samclip - /usr/local/bin/samclip
[17:24:15] Found seqtk - /usr/local/bin/seqtk
[17:24:15] Found parallel - /usr/local/bin/parallel
[17:24:15] Found freebayes - /usr/local/bin/freebayes
[17:24:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:15] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:15] Found gzip - /bin/gzip
[17:24:15] Found vt - /usr/local/bin/vt
[17:24:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:25:18] This is snippy 4.6.0Show full stderr[17:25:18] This is snippy 4.6.0
[17:25:18] Written by Torsten Seemann
[17:25:18] Obtained from https://github.com/tseemann/snippy
[17:25:18] Detected operating system: linux
[17:25:18] Enabling bundled linux tools.
[17:25:18] Found bwa - /usr/local/bin/bwa
[17:25:18] Found bcftools - /usr/local/bin/bcftools
[17:25:18] Found samtools - /usr/local/bin/samtools
[17:25:18] Found java - /usr/local/bin/java
[17:25:18] Found snpEff - /usr/local/bin/snpEff
[17:25:18] Found samclip - /usr/local/bin/samclip
[17:25:18] Found seqtk - /usr/local/bin/seqtk
[17:25:18] Found parallel - /usr/local/bin/parallel
[17:25:18] Found freebayes - /usr/local/bin/freebayes
[17:25:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:18] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:18] Found gzip - /bin/gzip
[17:25:18] Found vt - /usr/local/bin/vt
[17:25:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:25:36] This is snippy 4.6.0Show full stderr[17:25:36] This is snippy 4.6.0
[17:25:36] Written by Torsten Seemann
[17:25:36] Obtained from https://github.com/tseemann/snippy
[17:25:36] Detected operating system: linux
[17:25:36] Enabling bundled linux tools.
[17:25:36] Found bwa - /usr/local/bin/bwa
[17:25:36] Found bcftools - /usr/local/bin/bcftools
[17:25:36] Found samtools - /usr/local/bin/samtools
[17:25:36] Found java - /usr/local/bin/java
[17:25:36] Found snpEff - /usr/local/bin/snpEff
[17:25:36] Found samclip - /usr/local/bin/samclip
[17:25:36] Found seqtk - /usr/local/bin/seqtk
[17:25:36] Found parallel - /usr/local/bin/parallel
[17:25:36] Found freebayes - /usr/local/bin/freebayes
[17:25:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:36] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:36] Found gzip - /bin/gzip
[17:25:36] Found vt - /usr/local/bin/vt
[17:25:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:25:51] This is snippy 4.6.0Show full stderr[17:25:51] This is snippy 4.6.0
[17:25:51] Written by Torsten Seemann
[17:25:51] Obtained from https://github.com/tseemann/snippy
[17:25:51] Detected operating system: linux
[17:25:51] Enabling bundled linux tools.
[17:25:51] Found bwa - /usr/local/bin/bwa
[17:25:51] Found bcftools - /usr/local/bin/bcftools
[17:25:51] Found samtools - /usr/local/bin/samtools
[17:25:51] Found java - /usr/local/bin/java
[17:25:51] Found snpEff - /usr/local/bin/snpEff
[17:25:51] Found samclip - /usr/local/bin/samclip
[17:25:51] Found seqtk - /usr/local/bin/seqtk
[17:25:51] Found parallel - /usr/local/bin/parallel
[17:25:51] Found freebayes - /usr/local/bin/freebayes
[17:25:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:51] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:51] Found gzip - /bin/gzip
[17:25:51] Found vt - /usr/local/bin/vt
[17:25:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:30:19] This is snippy 4.6.0Show full stderr[17:30:19] This is snippy 4.6.0
[17:30:19] Written by Torsten Seemann
[17:30:19] Obtained from https://github.com/tseemann/snippy
[17:30:19] Detected operating system: linux
[17:30:19] Enabling bundled linux tools.
[17:30:19] Found bwa - /usr/local/bin/bwa
[17:30:19] Found bcftools - /usr/local/bin/bcftools
[17:30:19] Found samtools - /usr/local/bin/samtools
[17:30:19] Found java - /usr/local/bin/java
[17:30:19] Found snpEff - /usr/local/bin/snpEff
[17:30:19] Found samclip - /usr/local/bin/samclip
[17:30:19] Found seqtk - /usr/local/bin/seqtk
[17:30:19] Found parallel - /usr/local/bin/parallel
[17:30:19] Found freebayes - /usr/local/bin/freebayes
[17:30:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:30:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:30:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:30:19] Found vcfuniq - /usr/local/bin/vcfuniq
[17:30:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:30:19] Found gzip - /bin/gzip
[17:30:19] Found vt - /usr/local/bin/vt
[17:30:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:30:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:30:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:30:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:30:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:30:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:30:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:30:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:27:22] This is snippy 4.6.0Show full stderr[17:27:22] This is snippy 4.6.0
[17:27:22] Written by Torsten Seemann
[17:27:22] Obtained from https://github.com/tseemann/snippy
[17:27:22] Detected operating system: linux
[17:27:22] Enabling bundled linux tools.
[17:27:22] Found bwa - /usr/local/bin/bwa
[17:27:22] Found bcftools - /usr/local/bin/bcftools
[17:27:22] Found samtools - /usr/local/bin/samtools
[17:27:23] Found java - /usr/local/bin/java
[17:27:23] Found snpEff - /usr/local/bin/snpEff
[17:27:23] Found samclip - /usr/local/bin/samclip
[17:27:23] Found seqtk - /usr/local/bin/seqtk
[17:27:23] Found parallel - /usr/local/bin/parallel
[17:27:23] Found freebayes - /usr/local/bin/freebayes
[17:27:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:27:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:27:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:27:23] Found vcfuniq - /usr/local/bin/vcfuniq
[17:27:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:27:23] Found gzip - /bin/gzip
[17:27:23] Found vt - /usr/local/bin/vt
[17:27:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:27:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:27:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:27:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:27:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:27:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:27:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:27:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:27:40] This is snippy 4.6.0Show full stderr[17:27:40] This is snippy 4.6.0
[17:27:40] Written by Torsten Seemann
[17:27:40] Obtained from https://github.com/tseemann/snippy
[17:27:40] Detected operating system: linux
[17:27:40] Enabling bundled linux tools.
[17:27:40] Found bwa - /usr/local/bin/bwa
[17:27:40] Found bcftools - /usr/local/bin/bcftools
[17:27:40] Found samtools - /usr/local/bin/samtools
[17:27:40] Found java - /usr/local/bin/java
[17:27:40] Found snpEff - /usr/local/bin/snpEff
[17:27:40] Found samclip - /usr/local/bin/samclip
[17:27:40] Found seqtk - /usr/local/bin/seqtk
[17:27:41] Found parallel - /usr/local/bin/parallel
[17:27:41] Found freebayes - /usr/local/bin/freebayes
[17:27:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:27:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:27:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:27:41] Found vcfuniq - /usr/local/bin/vcfuniq
[17:27:41] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:27:41] Found gzip - /bin/gzip
[17:27:41] Found vt - /usr/local/bin/vt
[17:27:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:27:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:27:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:27:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:27:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:27:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:27:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:27:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:23:49] This is snippy 4.6.0Show full stderr[17:23:49] This is snippy 4.6.0
[17:23:49] Written by Torsten Seemann
[17:23:49] Obtained from https://github.com/tseemann/snippy
[17:23:49] Detected operating system: linux
[17:23:49] Enabling bundled linux tools.
[17:23:49] Found bwa - /usr/local/bin/bwa
[17:23:49] Found bcftools - /usr/local/bin/bcftools
[17:23:49] Found samtools - /usr/local/bin/samtools
[17:23:49] Found java - /usr/local/bin/java
[17:23:49] Found snpEff - /usr/local/bin/snpEff
[17:23:49] Found samclip - /usr/local/bin/samclip
[17:23:49] Found seqtk - /usr/local/bin/seqtk
[17:23:49] Found parallel - /usr/local/bin/parallel
[17:23:49] Found freebayes - /usr/local/bin/freebayes
[17:23:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:23:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:23:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:23:49] Found vcfuniq - /usr/local/bin/vcfuniq
[17:23:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:23:49] Found gzip - /bin/gzip
[17:23:49] Found vt - /usr/local/bin/vt
[17:23:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:23:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:23:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:23:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:23:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:23:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:23:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:23:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:16] This is snippy 4.6.0Show full stderr[17:24:16] This is snippy 4.6.0
[17:24:16] Written by Torsten Seemann
[17:24:16] Obtained from https://github.com/tseemann/snippy
[17:24:16] Detected operating system: linux
[17:24:16] Enabling bundled linux tools.
[17:24:16] Found bwa - /usr/local/bin/bwa
[17:24:16] Found bcftools - /usr/local/bin/bcftools
[17:24:16] Found samtools - /usr/local/bin/samtools
[17:24:16] Found java - /usr/local/bin/java
[17:24:16] Found snpEff - /usr/local/bin/snpEff
[17:24:16] Found samclip - /usr/local/bin/samclip
[17:24:16] Found seqtk - /usr/local/bin/seqtk
[17:24:16] Found parallel - /usr/local/bin/parallel
[17:24:16] Found freebayes - /usr/local/bin/freebayes
[17:24:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:16] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:16] Found gzip - /bin/gzip
[17:24:16] Found vt - /usr/local/bin/vt
[17:24:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:30:38] This is snippy 4.6.0Show full stderr[17:30:38] This is snippy 4.6.0
[17:30:38] Written by Torsten Seemann
[17:30:38] Obtained from https://github.com/tseemann/snippy
[17:30:38] Detected operating system: linux
[17:30:38] Enabling bundled linux tools.
[17:30:38] Found bwa - /usr/local/bin/bwa
[17:30:38] Found bcftools - /usr/local/bin/bcftools
[17:30:39] Found samtools - /usr/local/bin/samtools
[17:30:39] Found java - /usr/local/bin/java
[17:30:39] Found snpEff - /usr/local/bin/snpEff
[17:30:39] Found samclip - /usr/local/bin/samclip
[17:30:39] Found seqtk - /usr/local/bin/seqtk
[17:30:39] Found parallel - /usr/local/bin/parallel
[17:30:39] Found freebayes - /usr/local/bin/freebayes
[17:30:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:30:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:30:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:30:39] Found vcfuniq - /usr/local/bin/vcfuniq
[17:30:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:30:39] Found gzip - /bin/gzip
[17:30:39] Found vt - /usr/local/bin/vt
[17:30:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:30:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:30:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:30:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:30:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:30:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:30:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:30:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:36] This is snippy 4.6.0Show full stderr[17:24:36] This is snippy 4.6.0
[17:24:36] Written by Torsten Seemann
[17:24:36] Obtained from https://github.com/tseemann/snippy
[17:24:36] Detected operating system: linux
[17:24:36] Enabling bundled linux tools.
[17:24:36] Found bwa - /usr/local/bin/bwa
[17:24:36] Found bcftools - /usr/local/bin/bcftools
[17:24:36] Found samtools - /usr/local/bin/samtools
[17:24:36] Found java - /usr/local/bin/java
[17:24:36] Found snpEff - /usr/local/bin/snpEff
[17:24:36] Found samclip - /usr/local/bin/samclip
[17:24:36] Found seqtk - /usr/local/bin/seqtk
[17:24:36] Found parallel - /usr/local/bin/parallel
[17:24:36] Found freebayes - /usr/local/bin/freebayes
[17:24:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:36] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:36] Found gzip - /bin/gzip
[17:24:36] Found vt - /usr/local/bin/vt
[17:24:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:25:08] This is snippy 4.6.0Show full stderr[17:25:08] This is snippy 4.6.0
[17:25:08] Written by Torsten Seemann
[17:25:08] Obtained from https://github.com/tseemann/snippy
[17:25:08] Detected operating system: linux
[17:25:08] Enabling bundled linux tools.
[17:25:08] Found bwa - /usr/local/bin/bwa
[17:25:08] Found bcftools - /usr/local/bin/bcftools
[17:25:08] Found samtools - /usr/local/bin/samtools
[17:25:08] Found java - /usr/local/bin/java
[17:25:08] Found snpEff - /usr/local/bin/snpEff
[17:25:08] Found samclip - /usr/local/bin/samclip
[17:25:08] Found seqtk - /usr/local/bin/seqtk
[17:25:08] Found parallel - /usr/local/bin/parallel
[17:25:08] Found freebayes - /usr/local/bin/freebayes
[17:25:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:08] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:08] Found gzip - /bin/gzip
[17:25:08] Found vt - /usr/local/bin/vt
[17:25:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:25:45] This is snippy 4.6.0Show full stderr[17:25:45] This is snippy 4.6.0
[17:25:45] Written by Torsten Seemann
[17:25:45] Obtained from https://github.com/tseemann/snippy
[17:25:45] Detected operating system: linux
[17:25:45] Enabling bundled linux tools.
[17:25:45] Found bwa - /usr/local/bin/bwa
[17:25:45] Found bcftools - /usr/local/bin/bcftools
[17:25:45] Found samtools - /usr/local/bin/samtools
[17:25:45] Found java - /usr/local/bin/java
[17:25:45] Found snpEff - /usr/local/bin/snpEff
[17:25:45] Found samclip - /usr/local/bin/samclip
[17:25:45] Found seqtk - /usr/local/bin/seqtk
[17:25:45] Found parallel - /usr/local/bin/parallel
[17:25:45] Found freebayes - /usr/local/bin/freebayes
[17:25:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:46] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:46] Found gzip - /bin/gzip
[17:25:46] Found vt - /usr/local/bin/vt
[17:25:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:25:42] This is snippy 4.6.0Show full stderr[17:25:42] This is snippy 4.6.0
[17:25:42] Written by Torsten Seemann
[17:25:42] Obtained from https://github.com/tseemann/snippy
[17:25:42] Detected operating system: linux
[17:25:42] Enabling bundled linux tools.
[17:25:42] Found bwa - /usr/local/bin/bwa
[17:25:42] Found bcftools - /usr/local/bin/bcftools
[17:25:42] Found samtools - /usr/local/bin/samtools
[17:25:42] Found java - /usr/local/bin/java
[17:25:42] Found snpEff - /usr/local/bin/snpEff
[17:25:42] Found samclip - /usr/local/bin/samclip
[17:25:42] Found seqtk - /usr/local/bin/seqtk
[17:25:42] Found parallel - /usr/local/bin/parallel
[17:25:42] Found freebayes - /usr/local/bin/freebayes
[17:25:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:42] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:42] Found gzip - /bin/gzip
[17:25:42] Found vt - /usr/local/bin/vt
[17:25:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:55:24] This is snippy 4.6.0Show full stderr[17:55:24] This is snippy 4.6.0
[17:55:24] Written by Torsten Seemann
[17:55:24] Obtained from https://github.com/tseemann/snippy
[17:55:24] Detected operating system: linux
[17:55:24] Enabling bundled linux tools.
[17:55:24] Found bwa - /usr/local/bin/bwa
[17:55:24] Found bcftools - /usr/local/bin/bcftools
[17:55:24] Found samtools - /usr/local/bin/samtools
[17:55:24] Found java - /usr/local/bin/java
[17:55:24] Found snpEff - /usr/local/bin/snpEff
[17:55:24] Found samclip - /usr/local/bin/samclip
[17:55:24] Found seqtk - /usr/local/bin/seqtk
[17:55:24] Found parallel - /usr/local/bin/parallel
[17:55:24] Found freebayes - /usr/local/bin/freebayes
[17:55:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:55:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:55:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:55:24] Found vcfuniq - /usr/local/bin/vcfuniq
[17:55:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:55:24] Found gzip - /bin/gzip
[17:55:24] Found vt - /usr/local/bin/vt
[17:55:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:55:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:55:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:55:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:55:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:55:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:55:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:55:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:58:03] This is snippy 4.6.0Show full stderr[17:58:03] This is snippy 4.6.0
[17:58:03] Written by Torsten Seemann
[17:58:03] Obtained from https://github.com/tseemann/snippy
[17:58:03] Detected operating system: linux
[17:58:03] Enabling bundled linux tools.
[17:58:03] Found bwa - /usr/local/bin/bwa
[17:58:03] Found bcftools - /usr/local/bin/bcftools
[17:58:04] Found samtools - /usr/local/bin/samtools
[17:58:04] Found java - /usr/local/bin/java
[17:58:04] Found snpEff - /usr/local/bin/snpEff
[17:58:04] Found samclip - /usr/local/bin/samclip
[17:58:04] Found seqtk - /usr/local/bin/seqtk
[17:58:04] Found parallel - /usr/local/bin/parallel
[17:58:04] Found freebayes - /usr/local/bin/freebayes
[17:58:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:58:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:58:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:58:04] Found vcfuniq - /usr/local/bin/vcfuniq
[17:58:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:58:04] Found gzip - /bin/gzip
[17:58:04] Found vt - /usr/local/bin/vt
[17:58:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:58:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:58:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:58:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:58:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:58:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:58:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:58:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:09] This is snippy 4.6.0Show full stderr[17:26:09] This is snippy 4.6.0
[17:26:09] Written by Torsten Seemann
[17:26:09] Obtained from https://github.com/tseemann/snippy
[17:26:09] Detected operating system: linux
[17:26:09] Enabling bundled linux tools.
[17:26:09] Found bwa - /usr/local/bin/bwa
[17:26:09] Found bcftools - /usr/local/bin/bcftools
[17:26:09] Found samtools - /usr/local/bin/samtools
[17:26:09] Found java - /usr/local/bin/java
[17:26:09] Found snpEff - /usr/local/bin/snpEff
[17:26:09] Found samclip - /usr/local/bin/samclip
[17:26:09] Found seqtk - /usr/local/bin/seqtk
[17:26:09] Found parallel - /usr/local/bin/parallel
[17:26:09] Found freebayes - /usr/local/bin/freebayes
[17:26:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:09] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:09] Found gzip - /bin/gzip
[17:26:09] Found vt - /usr/local/bin/vt
[17:26:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:58:10] This is snippy 4.6.0Show full stderr[17:58:10] This is snippy 4.6.0
[17:58:10] Written by Torsten Seemann
[17:58:10] Obtained from https://github.com/tseemann/snippy
[17:58:10] Detected operating system: linux
[17:58:10] Enabling bundled linux tools.
[17:58:10] Found bwa - /usr/local/bin/bwa
[17:58:10] Found bcftools - /usr/local/bin/bcftools
[17:58:10] Found samtools - /usr/local/bin/samtools
[17:58:10] Found java - /usr/local/bin/java
[17:58:10] Found snpEff - /usr/local/bin/snpEff
[17:58:10] Found samclip - /usr/local/bin/samclip
[17:58:10] Found seqtk - /usr/local/bin/seqtk
[17:58:10] Found parallel - /usr/local/bin/parallel
[17:58:10] Found freebayes - /usr/local/bin/freebayes
[17:58:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:58:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:58:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:58:10] Found vcfuniq - /usr/local/bin/vcfuniq
[17:58:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:58:10] Found gzip - /bin/gzip
[17:58:10] Found vt - /usr/local/bin/vt
[17:58:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:58:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:58:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:58:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:58:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:58:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:58:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:58:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:36] This is snippy 4.6.0Show full stderr[17:26:36] This is snippy 4.6.0
[17:26:36] Written by Torsten Seemann
[17:26:36] Obtained from https://github.com/tseemann/snippy
[17:26:36] Detected operating system: linux
[17:26:36] Enabling bundled linux tools.
[17:26:36] Found bwa - /usr/local/bin/bwa
[17:26:36] Found bcftools - /usr/local/bin/bcftools
[17:26:36] Found samtools - /usr/local/bin/samtools
[17:26:36] Found java - /usr/local/bin/java
[17:26:36] Found snpEff - /usr/local/bin/snpEff
[17:26:36] Found samclip - /usr/local/bin/samclip
[17:26:36] Found seqtk - /usr/local/bin/seqtk
[17:26:36] Found parallel - /usr/local/bin/parallel
[17:26:36] Found freebayes - /usr/local/bin/freebayes
[17:26:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:37] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:37] Found gzip - /bin/gzip
[17:26:37] Found vt - /usr/local/bin/vt
[17:26:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:21] This is snippy 4.6.0Show full stderr[17:24:21] This is snippy 4.6.0
[17:24:21] Written by Torsten Seemann
[17:24:21] Obtained from https://github.com/tseemann/snippy
[17:24:21] Detected operating system: linux
[17:24:21] Enabling bundled linux tools.
[17:24:21] Found bwa - /usr/local/bin/bwa
[17:24:21] Found bcftools - /usr/local/bin/bcftools
[17:24:21] Found samtools - /usr/local/bin/samtools
[17:24:21] Found java - /usr/local/bin/java
[17:24:21] Found snpEff - /usr/local/bin/snpEff
[17:24:21] Found samclip - /usr/local/bin/samclip
[17:24:21] Found seqtk - /usr/local/bin/seqtk
[17:24:21] Found parallel - /usr/local/bin/parallel
[17:24:21] Found freebayes - /usr/local/bin/freebayes
[17:24:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:21] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:21] Found gzip - /bin/gzip
[17:24:21] Found vt - /usr/local/bin/vt
[17:24:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:42] This is snippy 4.6.0Show full stderr[17:24:42] This is snippy 4.6.0
[17:24:42] Written by Torsten Seemann
[17:24:42] Obtained from https://github.com/tseemann/snippy
[17:24:42] Detected operating system: linux
[17:24:42] Enabling bundled linux tools.
[17:24:42] Found bwa - /usr/local/bin/bwa
[17:24:42] Found bcftools - /usr/local/bin/bcftools
[17:24:42] Found samtools - /usr/local/bin/samtools
[17:24:42] Found java - /usr/local/bin/java
[17:24:42] Found snpEff - /usr/local/bin/snpEff
[17:24:42] Found samclip - /usr/local/bin/samclip
[17:24:42] Found seqtk - /usr/local/bin/seqtk
[17:24:42] Found parallel - /usr/local/bin/parallel
[17:24:42] Found freebayes - /usr/local/bin/freebayes
[17:24:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:42] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:42] Found gzip - /bin/gzip
[17:24:42] Found vt - /usr/local/bin/vt
[17:24:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:48] This is snippy 4.6.0Show full stderr[17:24:48] This is snippy 4.6.0
[17:24:48] Written by Torsten Seemann
[17:24:48] Obtained from https://github.com/tseemann/snippy
[17:24:48] Detected operating system: linux
[17:24:48] Enabling bundled linux tools.
[17:24:48] Found bwa - /usr/local/bin/bwa
[17:24:48] Found bcftools - /usr/local/bin/bcftools
[17:24:48] Found samtools - /usr/local/bin/samtools
[17:24:48] Found java - /usr/local/bin/java
[17:24:48] Found snpEff - /usr/local/bin/snpEff
[17:24:48] Found samclip - /usr/local/bin/samclip
[17:24:48] Found seqtk - /usr/local/bin/seqtk
[17:24:48] Found parallel - /usr/local/bin/parallel
[17:24:48] Found freebayes - /usr/local/bin/freebayes
[17:24:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:48] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:49] Found gzip - /bin/gzip
[17:24:49] Found vt - /usr/local/bin/vt
[17:24:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:57] This is snippy 4.6.0Show full stderr[17:24:57] This is snippy 4.6.0
[17:24:57] Written by Torsten Seemann
[17:24:57] Obtained from https://github.com/tseemann/snippy
[17:24:57] Detected operating system: linux
[17:24:57] Enabling bundled linux tools.
[17:24:57] Found bwa - /usr/local/bin/bwa
[17:24:57] Found bcftools - /usr/local/bin/bcftools
[17:24:57] Found samtools - /usr/local/bin/samtools
[17:24:57] Found java - /usr/local/bin/java
[17:24:57] Found snpEff - /usr/local/bin/snpEff
[17:24:57] Found samclip - /usr/local/bin/samclip
[17:24:57] Found seqtk - /usr/local/bin/seqtk
[17:24:57] Found parallel - /usr/local/bin/parallel
[17:24:57] Found freebayes - /usr/local/bin/freebayes
[17:24:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:57] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:57] Found gzip - /bin/gzip
[17:24:57] Found vt - /usr/local/bin/vt
[17:24:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:36:39] This is snippy 4.6.0Show full stderr[17:36:39] This is snippy 4.6.0
[17:36:39] Written by Torsten Seemann
[17:36:39] Obtained from https://github.com/tseemann/snippy
[17:36:39] Detected operating system: linux
[17:36:39] Enabling bundled linux tools.
[17:36:39] Found bwa - /usr/local/bin/bwa
[17:36:39] Found bcftools - /usr/local/bin/bcftools
[17:36:39] Found samtools - /usr/local/bin/samtools
[17:36:39] Found java - /usr/local/bin/java
[17:36:39] Found snpEff - /usr/local/bin/snpEff
[17:36:39] Found samclip - /usr/local/bin/samclip
[17:36:39] Found seqtk - /usr/local/bin/seqtk
[17:36:39] Found parallel - /usr/local/bin/parallel
[17:36:39] Found freebayes - /usr/local/bin/freebayes
[17:36:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:36:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:36:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:36:39] Found vcfuniq - /usr/local/bin/vcfuniq
[17:36:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:36:39] Found gzip - /bin/gzip
[17:36:39] Found vt - /usr/local/bin/vt
[17:36:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:36:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:36:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:36:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:36:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:36:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:36:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:36:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:25:14] This is snippy 4.6.0Show full stderr[17:25:14] This is snippy 4.6.0
[17:25:14] Written by Torsten Seemann
[17:25:14] Obtained from https://github.com/tseemann/snippy
[17:25:14] Detected operating system: linux
[17:25:14] Enabling bundled linux tools.
[17:25:14] Found bwa - /usr/local/bin/bwa
[17:25:14] Found bcftools - /usr/local/bin/bcftools
[17:25:14] Found samtools - /usr/local/bin/samtools
[17:25:14] Found java - /usr/local/bin/java
[17:25:14] Found snpEff - /usr/local/bin/snpEff
[17:25:14] Found samclip - /usr/local/bin/samclip
[17:25:14] Found seqtk - /usr/local/bin/seqtk
[17:25:14] Found parallel - /usr/local/bin/parallel
[17:25:14] Found freebayes - /usr/local/bin/freebayes
[17:25:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:14] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:14] Found gzip - /bin/gzip
[17:25:14] Found vt - /usr/local/bin/vt
[17:25:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:42:49] This is snippy 4.6.0Show full stderr[17:42:49] This is snippy 4.6.0
[17:42:49] Written by Torsten Seemann
[17:42:49] Obtained from https://github.com/tseemann/snippy
[17:42:49] Detected operating system: linux
[17:42:49] Enabling bundled linux tools.
[17:42:49] Found bwa - /usr/local/bin/bwa
[17:42:49] Found bcftools - /usr/local/bin/bcftools
[17:42:49] Found samtools - /usr/local/bin/samtools
[17:42:49] Found java - /usr/local/bin/java
[17:42:49] Found snpEff - /usr/local/bin/snpEff
[17:42:49] Found samclip - /usr/local/bin/samclip
[17:42:49] Found seqtk - /usr/local/bin/seqtk
[17:42:49] Found parallel - /usr/local/bin/parallel
[17:42:49] Found freebayes - /usr/local/bin/freebayes
[17:42:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:42:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:42:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:42:49] Found vcfuniq - /usr/local/bin/vcfuniq
[17:42:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:42:49] Found gzip - /bin/gzip
[17:42:49] Found vt - /usr/local/bin/vt
[17:42:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:42:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:42:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:42:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:42:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:42:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:42:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:42:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:25:54] This is snippy 4.6.0Show full stderr[17:25:54] This is snippy 4.6.0
[17:25:54] Written by Torsten Seemann
[17:25:54] Obtained from https://github.com/tseemann/snippy
[17:25:54] Detected operating system: linux
[17:25:54] Enabling bundled linux tools.
[17:25:54] Found bwa - /usr/local/bin/bwa
[17:25:54] Found bcftools - /usr/local/bin/bcftools
[17:25:54] Found samtools - /usr/local/bin/samtools
[17:25:54] Found java - /usr/local/bin/java
[17:25:54] Found snpEff - /usr/local/bin/snpEff
[17:25:54] Found samclip - /usr/local/bin/samclip
[17:25:54] Found seqtk - /usr/local/bin/seqtk
[17:25:54] Found parallel - /usr/local/bin/parallel
[17:25:54] Found freebayes - /usr/local/bin/freebayes
[17:25:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:54] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:54] Found gzip - /bin/gzip
[17:25:54] Found vt - /usr/local/bin/vt
[17:25:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:07] This is snippy 4.6.0Show full stderr[17:26:07] This is snippy 4.6.0
[17:26:07] Written by Torsten Seemann
[17:26:07] Obtained from https://github.com/tseemann/snippy
[17:26:07] Detected operating system: linux
[17:26:07] Enabling bundled linux tools.
[17:26:07] Found bwa - /usr/local/bin/bwa
[17:26:07] Found bcftools - /usr/local/bin/bcftools
[17:26:07] Found samtools - /usr/local/bin/samtools
[17:26:07] Found java - /usr/local/bin/java
[17:26:07] Found snpEff - /usr/local/bin/snpEff
[17:26:07] Found samclip - /usr/local/bin/samclip
[17:26:07] Found seqtk - /usr/local/bin/seqtk
[17:26:07] Found parallel - /usr/local/bin/parallel
[17:26:08] Found freebayes - /usr/local/bin/freebayes
[17:26:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:08] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:08] Found gzip - /bin/gzip
[17:26:08] Found vt - /usr/local/bin/vt
[17:26:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:15] This is snippy 4.6.0Show full stderr[17:26:15] This is snippy 4.6.0
[17:26:15] Written by Torsten Seemann
[17:26:15] Obtained from https://github.com/tseemann/snippy
[17:26:15] Detected operating system: linux
[17:26:15] Enabling bundled linux tools.
[17:26:15] Found bwa - /usr/local/bin/bwa
[17:26:15] Found bcftools - /usr/local/bin/bcftools
[17:26:15] Found samtools - /usr/local/bin/samtools
[17:26:15] Found java - /usr/local/bin/java
[17:26:15] Found snpEff - /usr/local/bin/snpEff
[17:26:15] Found samclip - /usr/local/bin/samclip
[17:26:16] Found seqtk - /usr/local/bin/seqtk
[17:26:16] Found parallel - /usr/local/bin/parallel
[17:26:16] Found freebayes - /usr/local/bin/freebayes
[17:26:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:16] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:16] Found gzip - /bin/gzip
[17:26:16] Found vt - /usr/local/bin/vt
[17:26:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:17] This is snippy 4.6.0Show full stderr[17:24:17] This is snippy 4.6.0
[17:24:17] Written by Torsten Seemann
[17:24:17] Obtained from https://github.com/tseemann/snippy
[17:24:17] Detected operating system: linux
[17:24:17] Enabling bundled linux tools.
[17:24:17] Found bwa - /usr/local/bin/bwa
[17:24:17] Found bcftools - /usr/local/bin/bcftools
[17:24:17] Found samtools - /usr/local/bin/samtools
[17:24:17] Found java - /usr/local/bin/java
[17:24:17] Found snpEff - /usr/local/bin/snpEff
[17:24:17] Found samclip - /usr/local/bin/samclip
[17:24:17] Found seqtk - /usr/local/bin/seqtk
[17:24:17] Found parallel - /usr/local/bin/parallel
[17:24:17] Found freebayes - /usr/local/bin/freebayes
[17:24:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:17] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:17] Found gzip - /bin/gzip
[17:24:17] Found vt - /usr/local/bin/vt
[17:24:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:12] This is snippy 4.6.0Show full stderr[17:24:12] This is snippy 4.6.0
[17:24:12] Written by Torsten Seemann
[17:24:12] Obtained from https://github.com/tseemann/snippy
[17:24:12] Detected operating system: linux
[17:24:12] Enabling bundled linux tools.
[17:24:12] Found bwa - /usr/local/bin/bwa
[17:24:12] Found bcftools - /usr/local/bin/bcftools
[17:24:12] Found samtools - /usr/local/bin/samtools
[17:24:12] Found java - /usr/local/bin/java
[17:24:12] Found snpEff - /usr/local/bin/snpEff
[17:24:12] Found samclip - /usr/local/bin/samclip
[17:24:12] Found seqtk - /usr/local/bin/seqtk
[17:24:12] Found parallel - /usr/local/bin/parallel
[17:24:12] Found freebayes - /usr/local/bin/freebayes
[17:24:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:12] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:12] Found gzip - /bin/gzip
[17:24:12] Found vt - /usr/local/bin/vt
[17:24:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:45] This is snippy 4.6.0Show full stderr[17:24:45] This is snippy 4.6.0
[17:24:45] Written by Torsten Seemann
[17:24:45] Obtained from https://github.com/tseemann/snippy
[17:24:45] Detected operating system: linux
[17:24:45] Enabling bundled linux tools.
[17:24:45] Found bwa - /usr/local/bin/bwa
[17:24:45] Found bcftools - /usr/local/bin/bcftools
[17:24:45] Found samtools - /usr/local/bin/samtools
[17:24:45] Found java - /usr/local/bin/java
[17:24:45] Found snpEff - /usr/local/bin/snpEff
[17:24:45] Found samclip - /usr/local/bin/samclip
[17:24:45] Found seqtk - /usr/local/bin/seqtk
[17:24:45] Found parallel - /usr/local/bin/parallel
[17:24:45] Found freebayes - /usr/local/bin/freebayes
[17:24:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:45] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:45] Found gzip - /bin/gzip
[17:24:45] Found vt - /usr/local/bin/vt
[17:24:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:24:54] This is snippy 4.6.0Show full stderr[17:24:54] This is snippy 4.6.0
[17:24:54] Written by Torsten Seemann
[17:24:54] Obtained from https://github.com/tseemann/snippy
[17:24:54] Detected operating system: linux
[17:24:54] Enabling bundled linux tools.
[17:24:54] Found bwa - /usr/local/bin/bwa
[17:24:54] Found bcftools - /usr/local/bin/bcftools
[17:24:54] Found samtools - /usr/local/bin/samtools
[17:24:54] Found java - /usr/local/bin/java
[17:24:54] Found snpEff - /usr/local/bin/snpEff
[17:24:54] Found samclip - /usr/local/bin/samclip
[17:24:54] Found seqtk - /usr/local/bin/seqtk
[17:24:54] Found parallel - /usr/local/bin/parallel
[17:24:54] Found freebayes - /usr/local/bin/freebayes
[17:24:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:24:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:24:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:24:54] Found vcfuniq - /usr/local/bin/vcfuniq
[17:24:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:24:54] Found gzip - /bin/gzip
[17:24:54] Found vt - /usr/local/bin/vt
[17:24:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:24:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:24:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:24:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:24:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:24:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:24:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:24:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:25:00] This is snippy 4.6.0Show full stderr[17:25:00] This is snippy 4.6.0
[17:25:00] Written by Torsten Seemann
[17:25:00] Obtained from https://github.com/tseemann/snippy
[17:25:00] Detected operating system: linux
[17:25:00] Enabling bundled linux tools.
[17:25:01] Found bwa - /usr/local/bin/bwa
[17:25:01] Found bcftools - /usr/local/bin/bcftools
[17:25:01] Found samtools - /usr/local/bin/samtools
[17:25:01] Found java - /usr/local/bin/java
[17:25:01] Found snpEff - /usr/local/bin/snpEff
[17:25:01] Found samclip - /usr/local/bin/samclip
[17:25:01] Found seqtk - /usr/local/bin/seqtk
[17:25:01] Found parallel - /usr/local/bin/parallel
[17:25:01] Found freebayes - /usr/local/bin/freebayes
[17:25:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:01] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:01] Found gzip - /bin/gzip
[17:25:01] Found vt - /usr/local/bin/vt
[17:25:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:25:27] This is snippy 4.6.0Show full stderr[17:25:27] This is snippy 4.6.0
[17:25:27] Written by Torsten Seemann
[17:25:27] Obtained from https://github.com/tseemann/snippy
[17:25:27] Detected operating system: linux
[17:25:27] Enabling bundled linux tools.
[17:25:27] Found bwa - /usr/local/bin/bwa
[17:25:27] Found bcftools - /usr/local/bin/bcftools
[17:25:27] Found samtools - /usr/local/bin/samtools
[17:25:27] Found java - /usr/local/bin/java
[17:25:27] Found snpEff - /usr/local/bin/snpEff
[17:25:27] Found samclip - /usr/local/bin/samclip
[17:25:27] Found seqtk - /usr/local/bin/seqtk
[17:25:27] Found parallel - /usr/local/bin/parallel
[17:25:27] Found freebayes - /usr/local/bin/freebayes
[17:25:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:25:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:25:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:25:27] Found vcfuniq - /usr/local/bin/vcfuniq
[17:25:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:25:27] Found gzip - /bin/gzip
[17:25:27] Found vt - /usr/local/bin/vt
[17:25:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:25:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:25:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:25:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:25:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:25:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:25:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:25:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:49:06] This is snippy 4.6.0Show full stderr[17:49:06] This is snippy 4.6.0
[17:49:06] Written by Torsten Seemann
[17:49:06] Obtained from https://github.com/tseemann/snippy
[17:49:06] Detected operating system: linux
[17:49:06] Enabling bundled linux tools.
[17:49:06] Found bwa - /usr/local/bin/bwa
[17:49:06] Found bcftools - /usr/local/bin/bcftools
[17:49:06] Found samtools - /usr/local/bin/samtools
[17:49:07] Found java - /usr/local/bin/java
[17:49:07] Found snpEff - /usr/local/bin/snpEff
[17:49:07] Found samclip - /usr/local/bin/samclip
[17:49:07] Found seqtk - /usr/local/bin/seqtk
[17:49:07] Found parallel - /usr/local/bin/parallel
[17:49:07] Found freebayes - /usr/local/bin/freebayes
[17:49:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:49:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:49:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:49:07] Found vcfuniq - /usr/local/bin/vcfuniq
[17:49:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:49:07] Found gzip - /bin/gzip
[17:49:07] Found vt - /usr/local/bin/vt
[17:49:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:49:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:49:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:49:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:49:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:49:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:49:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:49:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:49:02] This is snippy 4.6.0Show full stderr[17:49:02] This is snippy 4.6.0
[17:49:02] Written by Torsten Seemann
[17:49:02] Obtained from https://github.com/tseemann/snippy
[17:49:02] Detected operating system: linux
[17:49:02] Enabling bundled linux tools.
[17:49:02] Found bwa - /usr/local/bin/bwa
[17:49:02] Found bcftools - /usr/local/bin/bcftools
[17:49:02] Found samtools - /usr/local/bin/samtools
[17:49:02] Found java - /usr/local/bin/java
[17:49:02] Found snpEff - /usr/local/bin/snpEff
[17:49:02] Found samclip - /usr/local/bin/samclip
[17:49:02] Found seqtk - /usr/local/bin/seqtk
[17:49:02] Found parallel - /usr/local/bin/parallel
[17:49:02] Found freebayes - /usr/local/bin/freebayes
[17:49:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:49:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:49:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:49:02] Found vcfuniq - /usr/local/bin/vcfuniq
[17:49:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:49:02] Found gzip - /bin/gzip
[17:49:02] Found vt - /usr/local/bin/vt
[17:49:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:49:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:49:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:49:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:49:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:49:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:49:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:49:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:55:03] This is snippy 4.6.0Show full stderr[17:55:03] This is snippy 4.6.0
[17:55:03] Written by Torsten Seemann
[17:55:03] Obtained from https://github.com/tseemann/snippy
[17:55:03] Detected operating system: linux
[17:55:03] Enabling bundled linux tools.
[17:55:03] Found bwa - /usr/local/bin/bwa
[17:55:03] Found bcftools - /usr/local/bin/bcftools
[17:55:03] Found samtools - /usr/local/bin/samtools
[17:55:03] Found java - /usr/local/bin/java
[17:55:03] Found snpEff - /usr/local/bin/snpEff
[17:55:03] Found samclip - /usr/local/bin/samclip
[17:55:03] Found seqtk - /usr/local/bin/seqtk
[17:55:03] Found parallel - /usr/local/bin/parallel
[17:55:03] Found freebayes - /usr/local/bin/freebayes
[17:55:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:55:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:55:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:55:03] Found vcfuniq - /usr/local/bin/vcfuniq
[17:55:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:55:03] Found gzip - /bin/gzip
[17:55:03] Found vt - /usr/local/bin/vt
[17:55:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:55:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:55:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:55:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:55:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:55:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:55:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:55:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:57:39] This is snippy 4.6.0Show full stderr[17:57:39] This is snippy 4.6.0
[17:57:39] Written by Torsten Seemann
[17:57:39] Obtained from https://github.com/tseemann/snippy
[17:57:39] Detected operating system: linux
[17:57:39] Enabling bundled linux tools.
[17:57:39] Found bwa - /usr/local/bin/bwa
[17:57:39] Found bcftools - /usr/local/bin/bcftools
[17:57:39] Found samtools - /usr/local/bin/samtools
[17:57:39] Found java - /usr/local/bin/java
[17:57:39] Found snpEff - /usr/local/bin/snpEff
[17:57:39] Found samclip - /usr/local/bin/samclip
[17:57:39] Found seqtk - /usr/local/bin/seqtk
[17:57:39] Found parallel - /usr/local/bin/parallel
[17:57:39] Found freebayes - /usr/local/bin/freebayes
[17:57:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:57:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:57:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:57:39] Found vcfuniq - /usr/local/bin/vcfuniq
[17:57:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:57:39] Found gzip - /bin/gzip
[17:57:39] Found vt - /usr/local/bin/vt
[17:57:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:57:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:57:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:57:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:57:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:57:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:57:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:57:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:01:36] This is snippy 4.6.0Show full stderr[18:01:36] This is snippy 4.6.0
[18:01:36] Written by Torsten Seemann
[18:01:36] Obtained from https://github.com/tseemann/snippy
[18:01:36] Detected operating system: linux
[18:01:36] Enabling bundled linux tools.
[18:01:36] Found bwa - /usr/local/bin/bwa
[18:01:36] Found bcftools - /usr/local/bin/bcftools
[18:01:36] Found samtools - /usr/local/bin/samtools
[18:01:36] Found java - /usr/local/bin/java
[18:01:36] Found snpEff - /usr/local/bin/snpEff
[18:01:36] Found samclip - /usr/local/bin/samclip
[18:01:36] Found seqtk - /usr/local/bin/seqtk
[18:01:36] Found parallel - /usr/local/bin/parallel
[18:01:36] Found freebayes - /usr/local/bin/freebayes
[18:01:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:01:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:01:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:01:36] Found vcfuniq - /usr/local/bin/vcfuniq
[18:01:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:01:36] Found gzip - /bin/gzip
[18:01:36] Found vt - /usr/local/bin/vt
[18:01:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:01:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:01:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:01:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:01:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:01:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:01:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:01:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:08] This is snippy 4.6.0Show full stderr[17:26:08] This is snippy 4.6.0
[17:26:08] Written by Torsten Seemann
[17:26:08] Obtained from https://github.com/tseemann/snippy
[17:26:08] Detected operating system: linux
[17:26:08] Enabling bundled linux tools.
[17:26:08] Found bwa - /usr/local/bin/bwa
[17:26:08] Found bcftools - /usr/local/bin/bcftools
[17:26:08] Found samtools - /usr/local/bin/samtools
[17:26:08] Found java - /usr/local/bin/java
[17:26:08] Found snpEff - /usr/local/bin/snpEff
[17:26:08] Found samclip - /usr/local/bin/samclip
[17:26:08] Found seqtk - /usr/local/bin/seqtk
[17:26:08] Found parallel - /usr/local/bin/parallel
[17:26:08] Found freebayes - /usr/local/bin/freebayes
[17:26:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:08] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:08] Found gzip - /bin/gzip
[17:26:08] Found vt - /usr/local/bin/vt
[17:26:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:23] This is snippy 4.6.0Show full stderr[17:26:23] This is snippy 4.6.0
[17:26:23] Written by Torsten Seemann
[17:26:23] Obtained from https://github.com/tseemann/snippy
[17:26:23] Detected operating system: linux
[17:26:23] Enabling bundled linux tools.
[17:26:23] Found bwa - /usr/local/bin/bwa
[17:26:23] Found bcftools - /usr/local/bin/bcftools
[17:26:23] Found samtools - /usr/local/bin/samtools
[17:26:23] Found java - /usr/local/bin/java
[17:26:23] Found snpEff - /usr/local/bin/snpEff
[17:26:23] Found samclip - /usr/local/bin/samclip
[17:26:23] Found seqtk - /usr/local/bin/seqtk
[17:26:23] Found parallel - /usr/local/bin/parallel
[17:26:23] Found freebayes - /usr/local/bin/freebayes
[17:26:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:23] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:23] Found gzip - /bin/gzip
[17:26:23] Found vt - /usr/local/bin/vt
[17:26:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:38] This is snippy 4.6.0Show full stderr[17:26:38] This is snippy 4.6.0
[17:26:38] Written by Torsten Seemann
[17:26:38] Obtained from https://github.com/tseemann/snippy
[17:26:38] Detected operating system: linux
[17:26:38] Enabling bundled linux tools.
[17:26:38] Found bwa - /usr/local/bin/bwa
[17:26:38] Found bcftools - /usr/local/bin/bcftools
[17:26:38] Found samtools - /usr/local/bin/samtools
[17:26:38] Found java - /usr/local/bin/java
[17:26:38] Found snpEff - /usr/local/bin/snpEff
[17:26:38] Found samclip - /usr/local/bin/samclip
[17:26:38] Found seqtk - /usr/local/bin/seqtk
[17:26:38] Found parallel - /usr/local/bin/parallel
[17:26:38] Found freebayes - /usr/local/bin/freebayes
[17:26:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:38] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:38] Found gzip - /bin/gzip
[17:26:38] Found vt - /usr/local/bin/vt
[17:26:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:42] This is snippy 4.6.0Show full stderr[17:26:42] This is snippy 4.6.0
[17:26:42] Written by Torsten Seemann
[17:26:42] Obtained from https://github.com/tseemann/snippy
[17:26:42] Detected operating system: linux
[17:26:42] Enabling bundled linux tools.
[17:26:42] Found bwa - /usr/local/bin/bwa
[17:26:42] Found bcftools - /usr/local/bin/bcftools
[17:26:42] Found samtools - /usr/local/bin/samtools
[17:26:42] Found java - /usr/local/bin/java
[17:26:42] Found snpEff - /usr/local/bin/snpEff
[17:26:42] Found samclip - /usr/local/bin/samclip
[17:26:42] Found seqtk - /usr/local/bin/seqtk
[17:26:42] Found parallel - /usr/local/bin/parallel
[17:26:42] Found freebayes - /usr/local/bin/freebayes
[17:26:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:42] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:42] Found gzip - /bin/gzip
[17:26:42] Found vt - /usr/local/bin/vt
[17:26:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:55] This is snippy 4.6.0Show full stderr[17:26:55] This is snippy 4.6.0
[17:26:55] Written by Torsten Seemann
[17:26:55] Obtained from https://github.com/tseemann/snippy
[17:26:55] Detected operating system: linux
[17:26:55] Enabling bundled linux tools.
[17:26:55] Found bwa - /usr/local/bin/bwa
[17:26:55] Found bcftools - /usr/local/bin/bcftools
[17:26:55] Found samtools - /usr/local/bin/samtools
[17:26:55] Found java - /usr/local/bin/java
[17:26:55] Found snpEff - /usr/local/bin/snpEff
[17:26:56] Found samclip - /usr/local/bin/samclip
[17:26:56] Found seqtk - /usr/local/bin/seqtk
[17:26:56] Found parallel - /usr/local/bin/parallel
[17:26:56] Found freebayes - /usr/local/bin/freebayes
[17:26:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:56] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:56] Found gzip - /bin/gzip
[17:26:56] Found vt - /usr/local/bin/vt
[17:26:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:27:12] This is snippy 4.6.0Show full stderr[17:27:12] This is snippy 4.6.0
[17:27:12] Written by Torsten Seemann
[17:27:12] Obtained from https://github.com/tseemann/snippy
[17:27:12] Detected operating system: linux
[17:27:12] Enabling bundled linux tools.
[17:27:12] Found bwa - /usr/local/bin/bwa
[17:27:12] Found bcftools - /usr/local/bin/bcftools
[17:27:12] Found samtools - /usr/local/bin/samtools
[17:27:12] Found java - /usr/local/bin/java
[17:27:12] Found snpEff - /usr/local/bin/snpEff
[17:27:12] Found samclip - /usr/local/bin/samclip
[17:27:12] Found seqtk - /usr/local/bin/seqtk
[17:27:12] Found parallel - /usr/local/bin/parallel
[17:27:12] Found freebayes - /usr/local/bin/freebayes
[17:27:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:27:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:27:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:27:12] Found vcfuniq - /usr/local/bin/vcfuniq
[17:27:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:27:12] Found gzip - /bin/gzip
[17:27:12] Found vt - /usr/local/bin/vt
[17:27:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:27:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:27:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:27:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:27:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:27:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:27:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:27:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:28:14] This is snippy 4.6.0Show full stderr[17:28:14] This is snippy 4.6.0
[17:28:14] Written by Torsten Seemann
[17:28:14] Obtained from https://github.com/tseemann/snippy
[17:28:14] Detected operating system: linux
[17:28:14] Enabling bundled linux tools.
[17:28:14] Found bwa - /usr/local/bin/bwa
[17:28:14] Found bcftools - /usr/local/bin/bcftools
[17:28:14] Found samtools - /usr/local/bin/samtools
[17:28:14] Found java - /usr/local/bin/java
[17:28:14] Found snpEff - /usr/local/bin/snpEff
[17:28:14] Found samclip - /usr/local/bin/samclip
[17:28:14] Found seqtk - /usr/local/bin/seqtk
[17:28:14] Found parallel - /usr/local/bin/parallel
[17:28:14] Found freebayes - /usr/local/bin/freebayes
[17:28:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:28:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:28:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:28:14] Found vcfuniq - /usr/local/bin/vcfuniq
[17:28:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:28:14] Found gzip - /bin/gzip
[17:28:14] Found vt - /usr/local/bin/vt
[17:28:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:28:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:28:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:28:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:28:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:28:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:28:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:28:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:28:26] This is snippy 4.6.0Show full stderr[17:28:26] This is snippy 4.6.0
[17:28:26] Written by Torsten Seemann
[17:28:26] Obtained from https://github.com/tseemann/snippy
[17:28:26] Detected operating system: linux
[17:28:26] Enabling bundled linux tools.
[17:28:26] Found bwa - /usr/local/bin/bwa
[17:28:26] Found bcftools - /usr/local/bin/bcftools
[17:28:26] Found samtools - /usr/local/bin/samtools
[17:28:26] Found java - /usr/local/bin/java
[17:28:26] Found snpEff - /usr/local/bin/snpEff
[17:28:26] Found samclip - /usr/local/bin/samclip
[17:28:26] Found seqtk - /usr/local/bin/seqtk
[17:28:26] Found parallel - /usr/local/bin/parallel
[17:28:26] Found freebayes - /usr/local/bin/freebayes
[17:28:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:28:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:28:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:28:27] Found vcfuniq - /usr/local/bin/vcfuniq
[17:28:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:28:27] Found gzip - /bin/gzip
[17:28:27] Found vt - /usr/local/bin/vt
[17:28:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:28:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:28:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:28:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:28:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:28:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:28:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:28:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:28:30] This is snippy 4.6.0Show full stderr[17:28:30] This is snippy 4.6.0
[17:28:30] Written by Torsten Seemann
[17:28:30] Obtained from https://github.com/tseemann/snippy
[17:28:30] Detected operating system: linux
[17:28:30] Enabling bundled linux tools.
[17:28:30] Found bwa - /usr/local/bin/bwa
[17:28:30] Found bcftools - /usr/local/bin/bcftools
[17:28:30] Found samtools - /usr/local/bin/samtools
[17:28:30] Found java - /usr/local/bin/java
[17:28:30] Found snpEff - /usr/local/bin/snpEff
[17:28:30] Found samclip - /usr/local/bin/samclip
[17:28:30] Found seqtk - /usr/local/bin/seqtk
[17:28:30] Found parallel - /usr/local/bin/parallel
[17:28:30] Found freebayes - /usr/local/bin/freebayes
[17:28:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:28:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:28:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:28:30] Found vcfuniq - /usr/local/bin/vcfuniq
[17:28:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:28:30] Found gzip - /bin/gzip
[17:28:30] Found vt - /usr/local/bin/vt
[17:28:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:28:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:28:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:28:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:28:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:28:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:28:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:28:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:29:19] This is snippy 4.6.0Show full stderr[17:29:19] This is snippy 4.6.0
[17:29:19] Written by Torsten Seemann
[17:29:19] Obtained from https://github.com/tseemann/snippy
[17:29:19] Detected operating system: linux
[17:29:19] Enabling bundled linux tools.
[17:29:19] Found bwa - /usr/local/bin/bwa
[17:29:19] Found bcftools - /usr/local/bin/bcftools
[17:29:19] Found samtools - /usr/local/bin/samtools
[17:29:19] Found java - /usr/local/bin/java
[17:29:19] Found snpEff - /usr/local/bin/snpEff
[17:29:19] Found samclip - /usr/local/bin/samclip
[17:29:19] Found seqtk - /usr/local/bin/seqtk
[17:29:19] Found parallel - /usr/local/bin/parallel
[17:29:19] Found freebayes - /usr/local/bin/freebayes
[17:29:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:29:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:29:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:29:19] Found vcfuniq - /usr/local/bin/vcfuniq
[17:29:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:29:19] Found gzip - /bin/gzip
[17:29:19] Found vt - /usr/local/bin/vt
[17:29:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:29:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:29:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:29:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:29:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:29:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:29:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:29:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:29:44] This is snippy 4.6.0Show full stderr[17:29:44] This is snippy 4.6.0
[17:29:44] Written by Torsten Seemann
[17:29:44] Obtained from https://github.com/tseemann/snippy
[17:29:44] Detected operating system: linux
[17:29:44] Enabling bundled linux tools.
[17:29:44] Found bwa - /usr/local/bin/bwa
[17:29:44] Found bcftools - /usr/local/bin/bcftools
[17:29:44] Found samtools - /usr/local/bin/samtools
[17:29:44] Found java - /usr/local/bin/java
[17:29:44] Found snpEff - /usr/local/bin/snpEff
[17:29:44] Found samclip - /usr/local/bin/samclip
[17:29:44] Found seqtk - /usr/local/bin/seqtk
[17:29:44] Found parallel - /usr/local/bin/parallel
[17:29:44] Found freebayes - /usr/local/bin/freebayes
[17:29:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:29:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:29:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:29:44] Found vcfuniq - /usr/local/bin/vcfuniq
[17:29:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:29:44] Found gzip - /bin/gzip
[17:29:44] Found vt - /usr/local/bin/vt
[17:29:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:29:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:29:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:29:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:29:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:29:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:29:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:29:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:29:45] This is snippy 4.6.0Show full stderr[17:29:45] This is snippy 4.6.0
[17:29:45] Written by Torsten Seemann
[17:29:45] Obtained from https://github.com/tseemann/snippy
[17:29:45] Detected operating system: linux
[17:29:45] Enabling bundled linux tools.
[17:29:46] Found bwa - /usr/local/bin/bwa
[17:29:46] Found bcftools - /usr/local/bin/bcftools
[17:29:46] Found samtools - /usr/local/bin/samtools
[17:29:46] Found java - /usr/local/bin/java
[17:29:46] Found snpEff - /usr/local/bin/snpEff
[17:29:46] Found samclip - /usr/local/bin/samclip
[17:29:46] Found seqtk - /usr/local/bin/seqtk
[17:29:46] Found parallel - /usr/local/bin/parallel
[17:29:46] Found freebayes - /usr/local/bin/freebayes
[17:29:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:29:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:29:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:29:46] Found vcfuniq - /usr/local/bin/vcfuniq
[17:29:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:29:46] Found gzip - /bin/gzip
[17:29:46] Found vt - /usr/local/bin/vt
[17:29:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:29:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:29:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:29:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:29:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:29:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:29:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:29:47] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:30:01] This is snippy 4.6.0Show full stderr[17:30:01] This is snippy 4.6.0
[17:30:01] Written by Torsten Seemann
[17:30:01] Obtained from https://github.com/tseemann/snippy
[17:30:01] Detected operating system: linux
[17:30:01] Enabling bundled linux tools.
[17:30:01] Found bwa - /usr/local/bin/bwa
[17:30:01] Found bcftools - /usr/local/bin/bcftools
[17:30:01] Found samtools - /usr/local/bin/samtools
[17:30:01] Found java - /usr/local/bin/java
[17:30:01] Found snpEff - /usr/local/bin/snpEff
[17:30:01] Found samclip - /usr/local/bin/samclip
[17:30:01] Found seqtk - /usr/local/bin/seqtk
[17:30:01] Found parallel - /usr/local/bin/parallel
[17:30:02] Found freebayes - /usr/local/bin/freebayes
[17:30:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:30:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:30:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:30:02] Found vcfuniq - /usr/local/bin/vcfuniq
[17:30:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:30:02] Found gzip - /bin/gzip
[17:30:02] Found vt - /usr/local/bin/vt
[17:30:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:30:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:30:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:30:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:30:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:30:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:30:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:30:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:30:07] This is snippy 4.6.0Show full stderr[17:30:07] This is snippy 4.6.0
[17:30:07] Written by Torsten Seemann
[17:30:07] Obtained from https://github.com/tseemann/snippy
[17:30:07] Detected operating system: linux
[17:30:07] Enabling bundled linux tools.
[17:30:07] Found bwa - /usr/local/bin/bwa
[17:30:07] Found bcftools - /usr/local/bin/bcftools
[17:30:08] Found samtools - /usr/local/bin/samtools
[17:30:08] Found java - /usr/local/bin/java
[17:30:08] Found snpEff - /usr/local/bin/snpEff
[17:30:08] Found samclip - /usr/local/bin/samclip
[17:30:08] Found seqtk - /usr/local/bin/seqtk
[17:30:08] Found parallel - /usr/local/bin/parallel
[17:30:08] Found freebayes - /usr/local/bin/freebayes
[17:30:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:30:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:30:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:30:08] Found vcfuniq - /usr/local/bin/vcfuniq
[17:30:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:30:08] Found gzip - /bin/gzip
[17:30:08] Found vt - /usr/local/bin/vt
[17:30:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:30:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:30:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:30:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:30:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:30:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:30:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:30:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:30:45] This is snippy 4.6.0Show full stderr[17:30:45] This is snippy 4.6.0
[17:30:45] Written by Torsten Seemann
[17:30:45] Obtained from https://github.com/tseemann/snippy
[17:30:45] Detected operating system: linux
[17:30:45] Enabling bundled linux tools.
[17:30:45] Found bwa - /usr/local/bin/bwa
[17:30:45] Found bcftools - /usr/local/bin/bcftools
[17:30:45] Found samtools - /usr/local/bin/samtools
[17:30:45] Found java - /usr/local/bin/java
[17:30:45] Found snpEff - /usr/local/bin/snpEff
[17:30:45] Found samclip - /usr/local/bin/samclip
[17:30:45] Found seqtk - /usr/local/bin/seqtk
[17:30:45] Found parallel - /usr/local/bin/parallel
[17:30:45] Found freebayes - /usr/local/bin/freebayes
[17:30:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:30:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:30:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:30:45] Found vcfuniq - /usr/local/bin/vcfuniq
[17:30:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:30:45] Found gzip - /bin/gzip
[17:30:45] Found vt - /usr/local/bin/vt
[17:30:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:30:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:30:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:30:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:30:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:30:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:30:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:30:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:27:58] This is snippy 4.6.0Show full stderr[17:27:58] This is snippy 4.6.0
[17:27:58] Written by Torsten Seemann
[17:27:58] Obtained from https://github.com/tseemann/snippy
[17:27:58] Detected operating system: linux
[17:27:58] Enabling bundled linux tools.
[17:27:58] Found bwa - /usr/local/bin/bwa
[17:27:58] Found bcftools - /usr/local/bin/bcftools
[17:27:58] Found samtools - /usr/local/bin/samtools
[17:27:58] Found java - /usr/local/bin/java
[17:27:58] Found snpEff - /usr/local/bin/snpEff
[17:27:59] Found samclip - /usr/local/bin/samclip
[17:27:59] Found seqtk - /usr/local/bin/seqtk
[17:27:59] Found parallel - /usr/local/bin/parallel
[17:27:59] Found freebayes - /usr/local/bin/freebayes
[17:27:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:27:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:27:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:27:59] Found vcfuniq - /usr/local/bin/vcfuniq
[17:27:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:27:59] Found gzip - /bin/gzip
[17:27:59] Found vt - /usr/local/bin/vt
[17:27:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:27:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:27:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:27:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:27:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:28:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:28:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:28:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:28:08] This is snippy 4.6.0Show full stderr[17:28:08] This is snippy 4.6.0
[17:28:08] Written by Torsten Seemann
[17:28:08] Obtained from https://github.com/tseemann/snippy
[17:28:08] Detected operating system: linux
[17:28:08] Enabling bundled linux tools.
[17:28:08] Found bwa - /usr/local/bin/bwa
[17:28:08] Found bcftools - /usr/local/bin/bcftools
[17:28:08] Found samtools - /usr/local/bin/samtools
[17:28:08] Found java - /usr/local/bin/java
[17:28:08] Found snpEff - /usr/local/bin/snpEff
[17:28:08] Found samclip - /usr/local/bin/samclip
[17:28:08] Found seqtk - /usr/local/bin/seqtk
[17:28:08] Found parallel - /usr/local/bin/parallel
[17:28:08] Found freebayes - /usr/local/bin/freebayes
[17:28:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:28:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:28:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:28:08] Found vcfuniq - /usr/local/bin/vcfuniq
[17:28:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:28:08] Found gzip - /bin/gzip
[17:28:08] Found vt - /usr/local/bin/vt
[17:28:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:28:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:28:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:28:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:28:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:28:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:28:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:28:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:28:02] This is snippy 4.6.0Show full stderr[17:28:02] This is snippy 4.6.0
[17:28:02] Written by Torsten Seemann
[17:28:02] Obtained from https://github.com/tseemann/snippy
[17:28:02] Detected operating system: linux
[17:28:02] Enabling bundled linux tools.
[17:28:02] Found bwa - /usr/local/bin/bwa
[17:28:02] Found bcftools - /usr/local/bin/bcftools
[17:28:02] Found samtools - /usr/local/bin/samtools
[17:28:02] Found java - /usr/local/bin/java
[17:28:02] Found snpEff - /usr/local/bin/snpEff
[17:28:02] Found samclip - /usr/local/bin/samclip
[17:28:02] Found seqtk - /usr/local/bin/seqtk
[17:28:02] Found parallel - /usr/local/bin/parallel
[17:28:02] Found freebayes - /usr/local/bin/freebayes
[17:28:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:28:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:28:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:28:02] Found vcfuniq - /usr/local/bin/vcfuniq
[17:28:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:28:02] Found gzip - /bin/gzip
[17:28:02] Found vt - /usr/local/bin/vt
[17:28:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:28:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:28:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:28:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:28:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:28:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:28:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:28:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:28:15] This is snippy 4.6.0Show full stderr[17:28:15] This is snippy 4.6.0
[17:28:15] Written by Torsten Seemann
[17:28:15] Obtained from https://github.com/tseemann/snippy
[17:28:15] Detected operating system: linux
[17:28:15] Enabling bundled linux tools.
[17:28:15] Found bwa - /usr/local/bin/bwa
[17:28:15] Found bcftools - /usr/local/bin/bcftools
[17:28:15] Found samtools - /usr/local/bin/samtools
[17:28:15] Found java - /usr/local/bin/java
[17:28:15] Found snpEff - /usr/local/bin/snpEff
[17:28:15] Found samclip - /usr/local/bin/samclip
[17:28:15] Found seqtk - /usr/local/bin/seqtk
[17:28:15] Found parallel - /usr/local/bin/parallel
[17:28:15] Found freebayes - /usr/local/bin/freebayes
[17:28:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:28:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:28:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:28:15] Found vcfuniq - /usr/local/bin/vcfuniq
[17:28:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:28:16] Found gzip - /bin/gzip
[17:28:16] Found vt - /usr/local/bin/vt
[17:28:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:28:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:28:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:28:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:28:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:28:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:28:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:28:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:28:33] This is snippy 4.6.0Show full stderr[17:28:33] This is snippy 4.6.0
[17:28:33] Written by Torsten Seemann
[17:28:33] Obtained from https://github.com/tseemann/snippy
[17:28:33] Detected operating system: linux
[17:28:33] Enabling bundled linux tools.
[17:28:33] Found bwa - /usr/local/bin/bwa
[17:28:33] Found bcftools - /usr/local/bin/bcftools
[17:28:33] Found samtools - /usr/local/bin/samtools
[17:28:33] Found java - /usr/local/bin/java
[17:28:33] Found snpEff - /usr/local/bin/snpEff
[17:28:33] Found samclip - /usr/local/bin/samclip
[17:28:33] Found seqtk - /usr/local/bin/seqtk
[17:28:33] Found parallel - /usr/local/bin/parallel
[17:28:33] Found freebayes - /usr/local/bin/freebayes
[17:28:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:28:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:28:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:28:33] Found vcfuniq - /usr/local/bin/vcfuniq
[17:28:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:28:33] Found gzip - /bin/gzip
[17:28:33] Found vt - /usr/local/bin/vt
[17:28:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:28:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:28:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:28:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:28:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:28:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:28:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:28:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:29:03] This is snippy 4.6.0Show full stderr[17:29:03] This is snippy 4.6.0
[17:29:03] Written by Torsten Seemann
[17:29:03] Obtained from https://github.com/tseemann/snippy
[17:29:03] Detected operating system: linux
[17:29:03] Enabling bundled linux tools.
[17:29:03] Found bwa - /usr/local/bin/bwa
[17:29:03] Found bcftools - /usr/local/bin/bcftools
[17:29:03] Found samtools - /usr/local/bin/samtools
[17:29:03] Found java - /usr/local/bin/java
[17:29:04] Found snpEff - /usr/local/bin/snpEff
[17:29:04] Found samclip - /usr/local/bin/samclip
[17:29:04] Found seqtk - /usr/local/bin/seqtk
[17:29:04] Found parallel - /usr/local/bin/parallel
[17:29:04] Found freebayes - /usr/local/bin/freebayes
[17:29:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:29:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:29:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:29:04] Found vcfuniq - /usr/local/bin/vcfuniq
[17:29:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:29:04] Found gzip - /bin/gzip
[17:29:04] Found vt - /usr/local/bin/vt
[17:29:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:29:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:29:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:29:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:29:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:29:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:29:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:29:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:28:42] This is snippy 4.6.0Show full stderr[17:28:42] This is snippy 4.6.0
[17:28:42] Written by Torsten Seemann
[17:28:42] Obtained from https://github.com/tseemann/snippy
[17:28:42] Detected operating system: linux
[17:28:42] Enabling bundled linux tools.
[17:28:42] Found bwa - /usr/local/bin/bwa
[17:28:42] Found bcftools - /usr/local/bin/bcftools
[17:28:42] Found samtools - /usr/local/bin/samtools
[17:28:42] Found java - /usr/local/bin/java
[17:28:42] Found snpEff - /usr/local/bin/snpEff
[17:28:42] Found samclip - /usr/local/bin/samclip
[17:28:43] Found seqtk - /usr/local/bin/seqtk
[17:28:43] Found parallel - /usr/local/bin/parallel
[17:28:43] Found freebayes - /usr/local/bin/freebayes
[17:28:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:28:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:28:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:28:43] Found vcfuniq - /usr/local/bin/vcfuniq
[17:28:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:28:43] Found gzip - /bin/gzip
[17:28:43] Found vt - /usr/local/bin/vt
[17:28:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:28:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:28:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:28:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:28:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:28:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:28:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:28:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:29:13] This is snippy 4.6.0Show full stderr[17:29:13] This is snippy 4.6.0
[17:29:13] Written by Torsten Seemann
[17:29:13] Obtained from https://github.com/tseemann/snippy
[17:29:13] Detected operating system: linux
[17:29:13] Enabling bundled linux tools.
[17:29:14] Found bwa - /usr/local/bin/bwa
[17:29:14] Found bcftools - /usr/local/bin/bcftools
[17:29:14] Found samtools - /usr/local/bin/samtools
[17:29:14] Found java - /usr/local/bin/java
[17:29:14] Found snpEff - /usr/local/bin/snpEff
[17:29:14] Found samclip - /usr/local/bin/samclip
[17:29:14] Found seqtk - /usr/local/bin/seqtk
[17:29:14] Found parallel - /usr/local/bin/parallel
[17:29:14] Found freebayes - /usr/local/bin/freebayes
[17:29:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:29:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:29:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:29:14] Found vcfuniq - /usr/local/bin/vcfuniq
[17:29:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:29:14] Found gzip - /bin/gzip
[17:29:14] Found vt - /usr/local/bin/vt
[17:29:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:29:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:29:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:29:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:29:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:29:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:29:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:29:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:30:05] This is snippy 4.6.0Show full stderr[17:30:05] This is snippy 4.6.0
[17:30:05] Written by Torsten Seemann
[17:30:05] Obtained from https://github.com/tseemann/snippy
[17:30:05] Detected operating system: linux
[17:30:05] Enabling bundled linux tools.
[17:30:05] Found bwa - /usr/local/bin/bwa
[17:30:05] Found bcftools - /usr/local/bin/bcftools
[17:30:05] Found samtools - /usr/local/bin/samtools
[17:30:05] Found java - /usr/local/bin/java
[17:30:05] Found snpEff - /usr/local/bin/snpEff
[17:30:05] Found samclip - /usr/local/bin/samclip
[17:30:05] Found seqtk - /usr/local/bin/seqtk
[17:30:05] Found parallel - /usr/local/bin/parallel
[17:30:05] Found freebayes - /usr/local/bin/freebayes
[17:30:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:30:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:30:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:30:05] Found vcfuniq - /usr/local/bin/vcfuniq
[17:30:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:30:05] Found gzip - /bin/gzip
[17:30:05] Found vt - /usr/local/bin/vt
[17:30:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:30:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:30:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:30:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:30:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:30:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:30:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:30:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:30:10] This is snippy 4.6.0Show full stderr[17:30:10] This is snippy 4.6.0
[17:30:10] Written by Torsten Seemann
[17:30:10] Obtained from https://github.com/tseemann/snippy
[17:30:10] Detected operating system: linux
[17:30:10] Enabling bundled linux tools.
[17:30:11] Found bwa - /usr/local/bin/bwa
[17:30:11] Found bcftools - /usr/local/bin/bcftools
[17:30:11] Found samtools - /usr/local/bin/samtools
[17:30:11] Found java - /usr/local/bin/java
[17:30:11] Found snpEff - /usr/local/bin/snpEff
[17:30:11] Found samclip - /usr/local/bin/samclip
[17:30:11] Found seqtk - /usr/local/bin/seqtk
[17:30:11] Found parallel - /usr/local/bin/parallel
[17:30:11] Found freebayes - /usr/local/bin/freebayes
[17:30:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:30:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:30:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:30:11] Found vcfuniq - /usr/local/bin/vcfuniq
[17:30:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:30:11] Found gzip - /bin/gzip
[17:30:11] Found vt - /usr/local/bin/vt
[17:30:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:30:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:30:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:30:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:30:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:30:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:30:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:30:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:30:54] This is snippy 4.6.0Show full stderr[17:30:54] This is snippy 4.6.0
[17:30:54] Written by Torsten Seemann
[17:30:54] Obtained from https://github.com/tseemann/snippy
[17:30:54] Detected operating system: linux
[17:30:54] Enabling bundled linux tools.
[17:30:54] Found bwa - /usr/local/bin/bwa
[17:30:54] Found bcftools - /usr/local/bin/bcftools
[17:30:54] Found samtools - /usr/local/bin/samtools
[17:30:54] Found java - /usr/local/bin/java
[17:30:54] Found snpEff - /usr/local/bin/snpEff
[17:30:54] Found samclip - /usr/local/bin/samclip
[17:30:54] Found seqtk - /usr/local/bin/seqtk
[17:30:54] Found parallel - /usr/local/bin/parallel
[17:30:54] Found freebayes - /usr/local/bin/freebayes
[17:30:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:30:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:30:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:30:54] Found vcfuniq - /usr/local/bin/vcfuniq
[17:30:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:30:54] Found gzip - /bin/gzip
[17:30:54] Found vt - /usr/local/bin/vt
[17:30:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:30:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:30:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:30:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:30:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:30:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:30:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:30:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:41] This is snippy 4.6.0Show full stderr[17:26:41] This is snippy 4.6.0
[17:26:41] Written by Torsten Seemann
[17:26:41] Obtained from https://github.com/tseemann/snippy
[17:26:41] Detected operating system: linux
[17:26:41] Enabling bundled linux tools.
[17:26:41] Found bwa - /usr/local/bin/bwa
[17:26:41] Found bcftools - /usr/local/bin/bcftools
[17:26:41] Found samtools - /usr/local/bin/samtools
[17:26:41] Found java - /usr/local/bin/java
[17:26:41] Found snpEff - /usr/local/bin/snpEff
[17:26:41] Found samclip - /usr/local/bin/samclip
[17:26:41] Found seqtk - /usr/local/bin/seqtk
[17:26:41] Found parallel - /usr/local/bin/parallel
[17:26:42] Found freebayes - /usr/local/bin/freebayes
[17:26:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:42] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:42] Found gzip - /bin/gzip
[17:26:42] Found vt - /usr/local/bin/vt
[17:26:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:26:52] This is snippy 4.6.0Show full stderr[17:26:52] This is snippy 4.6.0
[17:26:52] Written by Torsten Seemann
[17:26:52] Obtained from https://github.com/tseemann/snippy
[17:26:52] Detected operating system: linux
[17:26:52] Enabling bundled linux tools.
[17:26:52] Found bwa - /usr/local/bin/bwa
[17:26:52] Found bcftools - /usr/local/bin/bcftools
[17:26:52] Found samtools - /usr/local/bin/samtools
[17:26:52] Found java - /usr/local/bin/java
[17:26:52] Found snpEff - /usr/local/bin/snpEff
[17:26:52] Found samclip - /usr/local/bin/samclip
[17:26:52] Found seqtk - /usr/local/bin/seqtk
[17:26:52] Found parallel - /usr/local/bin/parallel
[17:26:52] Found freebayes - /usr/local/bin/freebayes
[17:26:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:26:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:26:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:26:52] Found vcfuniq - /usr/local/bin/vcfuniq
[17:26:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:26:52] Found gzip - /bin/gzip
[17:26:52] Found vt - /usr/local/bin/vt
[17:26:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:26:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:26:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:26:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:26:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:26:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:26:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:26:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:27:06] This is snippy 4.6.0Show full stderr[17:27:06] This is snippy 4.6.0
[17:27:06] Written by Torsten Seemann
[17:27:06] Obtained from https://github.com/tseemann/snippy
[17:27:06] Detected operating system: linux
[17:27:06] Enabling bundled linux tools.
[17:27:06] Found bwa - /usr/local/bin/bwa
[17:27:06] Found bcftools - /usr/local/bin/bcftools
[17:27:06] Found samtools - /usr/local/bin/samtools
[17:27:06] Found java - /usr/local/bin/java
[17:27:06] Found snpEff - /usr/local/bin/snpEff
[17:27:06] Found samclip - /usr/local/bin/samclip
[17:27:06] Found seqtk - /usr/local/bin/seqtk
[17:27:06] Found parallel - /usr/local/bin/parallel
[17:27:06] Found freebayes - /usr/local/bin/freebayes
[17:27:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:27:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:27:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:27:06] Found vcfuniq - /usr/local/bin/vcfuniq
[17:27:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:27:06] Found gzip - /bin/gzip
[17:27:06] Found vt - /usr/local/bin/vt
[17:27:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:27:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:27:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:27:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:27:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:27:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:27:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:27:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:27:09] This is snippy 4.6.0Show full stderr[17:27:09] This is snippy 4.6.0
[17:27:09] Written by Torsten Seemann
[17:27:09] Obtained from https://github.com/tseemann/snippy
[17:27:09] Detected operating system: linux
[17:27:09] Enabling bundled linux tools.
[17:27:09] Found bwa - /usr/local/bin/bwa
[17:27:09] Found bcftools - /usr/local/bin/bcftools
[17:27:09] Found samtools - /usr/local/bin/samtools
[17:27:09] Found java - /usr/local/bin/java
[17:27:09] Found snpEff - /usr/local/bin/snpEff
[17:27:09] Found samclip - /usr/local/bin/samclip
[17:27:09] Found seqtk - /usr/local/bin/seqtk
[17:27:09] Found parallel - /usr/local/bin/parallel
[17:27:09] Found freebayes - /usr/local/bin/freebayes
[17:27:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:27:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:27:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:27:09] Found vcfuniq - /usr/local/bin/vcfuniq
[17:27:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:27:09] Found gzip - /bin/gzip
[17:27:09] Found vt - /usr/local/bin/vt
[17:27:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:27:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:27:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:27:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:27:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:27:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:27:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:27:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:27:37] This is snippy 4.6.0Show full stderr[17:27:37] This is snippy 4.6.0
[17:27:37] Written by Torsten Seemann
[17:27:37] Obtained from https://github.com/tseemann/snippy
[17:27:37] Detected operating system: linux
[17:27:37] Enabling bundled linux tools.
[17:27:37] Found bwa - /usr/local/bin/bwa
[17:27:37] Found bcftools - /usr/local/bin/bcftools
[17:27:37] Found samtools - /usr/local/bin/samtools
[17:27:37] Found java - /usr/local/bin/java
[17:27:37] Found snpEff - /usr/local/bin/snpEff
[17:27:37] Found samclip - /usr/local/bin/samclip
[17:27:37] Found seqtk - /usr/local/bin/seqtk
[17:27:37] Found parallel - /usr/local/bin/parallel
[17:27:37] Found freebayes - /usr/local/bin/freebayes
[17:27:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:27:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:27:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:27:37] Found vcfuniq - /usr/local/bin/vcfuniq
[17:27:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:27:37] Found gzip - /bin/gzip
[17:27:37] Found vt - /usr/local/bin/vt
[17:27:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:27:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:27:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:27:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:27:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:27:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:27:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:27:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:27:39] This is snippy 4.6.0Show full stderr[17:27:39] This is snippy 4.6.0
[17:27:39] Written by Torsten Seemann
[17:27:39] Obtained from https://github.com/tseemann/snippy
[17:27:39] Detected operating system: linux
[17:27:39] Enabling bundled linux tools.
[17:27:39] Found bwa - /usr/local/bin/bwa
[17:27:39] Found bcftools - /usr/local/bin/bcftools
[17:27:39] Found samtools - /usr/local/bin/samtools
[17:27:39] Found java - /usr/local/bin/java
[17:27:39] Found snpEff - /usr/local/bin/snpEff
[17:27:39] Found samclip - /usr/local/bin/samclip
[17:27:39] Found seqtk - /usr/local/bin/seqtk
[17:27:39] Found parallel - /usr/local/bin/parallel
[17:27:39] Found freebayes - /usr/local/bin/freebayes
[17:27:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:27:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:27:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:27:39] Found vcfuniq - /usr/local/bin/vcfuniq
[17:27:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:27:39] Found gzip - /bin/gzip
[17:27:39] Found vt - /usr/local/bin/vt
[17:27:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:27:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:27:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:27:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:27:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:27:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:27:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:27:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:27:49] This is snippy 4.6.0Show full stderr[17:27:49] This is snippy 4.6.0
[17:27:49] Written by Torsten Seemann
[17:27:49] Obtained from https://github.com/tseemann/snippy
[17:27:49] Detected operating system: linux
[17:27:49] Enabling bundled linux tools.
[17:27:49] Found bwa - /usr/local/bin/bwa
[17:27:49] Found bcftools - /usr/local/bin/bcftools
[17:27:49] Found samtools - /usr/local/bin/samtools
[17:27:49] Found java - /usr/local/bin/java
[17:27:49] Found snpEff - /usr/local/bin/snpEff
[17:27:49] Found samclip - /usr/local/bin/samclip
[17:27:49] Found seqtk - /usr/local/bin/seqtk
[17:27:49] Found parallel - /usr/local/bin/parallel
[17:27:49] Found freebayes - /usr/local/bin/freebayes
[17:27:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:27:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:27:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:27:49] Found vcfuniq - /usr/local/bin/vcfuniq
[17:27:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:27:49] Found gzip - /bin/gzip
[17:27:49] Found vt - /usr/local/bin/vt
[17:27:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:27:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:27:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:27:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:27:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:27:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:27:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:27:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [18:03:21] This is snippy 4.6.0Show full stderr[18:03:21] This is snippy 4.6.0
[18:03:21] Written by Torsten Seemann
[18:03:21] Obtained from https://github.com/tseemann/snippy
[18:03:21] Detected operating system: linux
[18:03:21] Enabling bundled linux tools.
[18:03:21] Found bwa - /usr/local/bin/bwa
[18:03:21] Found bcftools - /usr/local/bin/bcftools
[18:03:21] Found samtools - /usr/local/bin/samtools
[18:03:21] Found java - /usr/local/bin/java
[18:03:21] Found snpEff - /usr/local/bin/snpEff
[18:03:21] Found samclip - /usr/local/bin/samclip
[18:03:21] Found seqtk - /usr/local/bin/seqtk
[18:03:21] Found parallel - /usr/local/bin/parallel
[18:03:21] Found freebayes - /usr/local/bin/freebayes
[18:03:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:03:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:03:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:03:22] Found vcfuniq - /usr/local/bin/vcfuniq
[18:03:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:03:22] Found gzip - /bin/gzip
[18:03:22] Found vt - /usr/local/bin/vt
[18:03:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:03:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:03:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:03:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:03:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:03:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:03:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:03:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:39:00] This is snippy 4.6.0Show full stderr[17:39:00] This is snippy 4.6.0
[17:39:00] Written by Torsten Seemann
[17:39:00] Obtained from https://github.com/tseemann/snippy
[17:39:00] Detected operating system: linux
[17:39:00] Enabling bundled linux tools.
[17:39:00] Found bwa - /usr/local/bin/bwa
[17:39:00] Found bcftools - /usr/local/bin/bcftools
[17:39:00] Found samtools - /usr/local/bin/samtools
[17:39:00] Found java - /usr/local/bin/java
[17:39:00] Found snpEff - /usr/local/bin/snpEff
[17:39:00] Found samclip - /usr/local/bin/samclip
[17:39:00] Found seqtk - /usr/local/bin/seqtk
[17:39:00] Found parallel - /usr/local/bin/parallel
[17:39:00] Found freebayes - /usr/local/bin/freebayes
[17:39:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:39:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:39:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:39:00] Found vcfuniq - /usr/local/bin/vcfuniq
[17:39:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:39:00] Found gzip - /bin/gzip
[17:39:00] Found vt - /usr/local/bin/vt
[17:39:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:39:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:39:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:39:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:39:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:39:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:39:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:39:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:39:33] This is snippy 4.6.0Show full stderr[17:39:33] This is snippy 4.6.0
[17:39:33] Written by Torsten Seemann
[17:39:33] Obtained from https://github.com/tseemann/snippy
[17:39:33] Detected operating system: linux
[17:39:33] Enabling bundled linux tools.
[17:39:33] Found bwa - /usr/local/bin/bwa
[17:39:33] Found bcftools - /usr/local/bin/bcftools
[17:39:33] Found samtools - /usr/local/bin/samtools
[17:39:33] Found java - /usr/local/bin/java
[17:39:33] Found snpEff - /usr/local/bin/snpEff
[17:39:33] Found samclip - /usr/local/bin/samclip
[17:39:33] Found seqtk - /usr/local/bin/seqtk
[17:39:33] Found parallel - /usr/local/bin/parallel
[17:39:33] Found freebayes - /usr/local/bin/freebayes
[17:39:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:39:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:39:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:39:33] Found vcfuniq - /usr/local/bin/vcfuniq
[17:39:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:39:33] Found gzip - /bin/gzip
[17:39:33] Found vt - /usr/local/bin/vt
[17:39:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:39:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:39:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:39:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:39:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:39:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:39:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:39:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:40:10] This is snippy 4.6.0Show full stderr[17:40:10] This is snippy 4.6.0
[17:40:10] Written by Torsten Seemann
[17:40:10] Obtained from https://github.com/tseemann/snippy
[17:40:10] Detected operating system: linux
[17:40:10] Enabling bundled linux tools.
[17:40:10] Found bwa - /usr/local/bin/bwa
[17:40:10] Found bcftools - /usr/local/bin/bcftools
[17:40:10] Found samtools - /usr/local/bin/samtools
[17:40:10] Found java - /usr/local/bin/java
[17:40:10] Found snpEff - /usr/local/bin/snpEff
[17:40:10] Found samclip - /usr/local/bin/samclip
[17:40:10] Found seqtk - /usr/local/bin/seqtk
[17:40:10] Found parallel - /usr/local/bin/parallel
[17:40:10] Found freebayes - /usr/local/bin/freebayes
[17:40:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:40:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:40:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:40:10] Found vcfuniq - /usr/local/bin/vcfuniq
[17:40:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:40:10] Found gzip - /bin/gzip
[17:40:10] Found vt - /usr/local/bin/vt
[17:40:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:40:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:40:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:40:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:40:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:40:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:40:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:40:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:40:16] This is snippy 4.6.0Show full stderr[17:40:16] This is snippy 4.6.0
[17:40:16] Written by Torsten Seemann
[17:40:16] Obtained from https://github.com/tseemann/snippy
[17:40:16] Detected operating system: linux
[17:40:16] Enabling bundled linux tools.
[17:40:16] Found bwa - /usr/local/bin/bwa
[17:40:16] Found bcftools - /usr/local/bin/bcftools
[17:40:16] Found samtools - /usr/local/bin/samtools
[17:40:16] Found java - /usr/local/bin/java
[17:40:16] Found snpEff - /usr/local/bin/snpEff
[17:40:17] Found samclip - /usr/local/bin/samclip
[17:40:17] Found seqtk - /usr/local/bin/seqtk
[17:40:17] Found parallel - /usr/local/bin/parallel
[17:40:17] Found freebayes - /usr/local/bin/freebayes
[17:40:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:40:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:40:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:40:17] Found vcfuniq - /usr/local/bin/vcfuniq
[17:40:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:40:17] Found gzip - /bin/gzip
[17:40:17] Found vt - /usr/local/bin/vt
[17:40:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:40:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:40:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:40:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:40:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:40:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:40:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:40:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:40:31] This is snippy 4.6.0Show full stderr[17:40:31] This is snippy 4.6.0
[17:40:31] Written by Torsten Seemann
[17:40:31] Obtained from https://github.com/tseemann/snippy
[17:40:31] Detected operating system: linux
[17:40:31] Enabling bundled linux tools.
[17:40:31] Found bwa - /usr/local/bin/bwa
[17:40:31] Found bcftools - /usr/local/bin/bcftools
[17:40:31] Found samtools - /usr/local/bin/samtools
[17:40:31] Found java - /usr/local/bin/java
[17:40:31] Found snpEff - /usr/local/bin/snpEff
[17:40:31] Found samclip - /usr/local/bin/samclip
[17:40:31] Found seqtk - /usr/local/bin/seqtk
[17:40:31] Found parallel - /usr/local/bin/parallel
[17:40:31] Found freebayes - /usr/local/bin/freebayes
[17:40:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:40:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:40:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:40:31] Found vcfuniq - /usr/local/bin/vcfuniq
[17:40:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:40:31] Found gzip - /bin/gzip
[17:40:31] Found vt - /usr/local/bin/vt
[17:40:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:40:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:40:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:40:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:40:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:40:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:40:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:40:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:40:54] This is snippy 4.6.0Show full stderr[17:40:54] This is snippy 4.6.0
[17:40:54] Written by Torsten Seemann
[17:40:54] Obtained from https://github.com/tseemann/snippy
[17:40:54] Detected operating system: linux
[17:40:54] Enabling bundled linux tools.
[17:40:54] Found bwa - /usr/local/bin/bwa
[17:40:54] Found bcftools - /usr/local/bin/bcftools
[17:40:54] Found samtools - /usr/local/bin/samtools
[17:40:54] Found java - /usr/local/bin/java
[17:40:54] Found snpEff - /usr/local/bin/snpEff
[17:40:54] Found samclip - /usr/local/bin/samclip
[17:40:54] Found seqtk - /usr/local/bin/seqtk
[17:40:54] Found parallel - /usr/local/bin/parallel
[17:40:54] Found freebayes - /usr/local/bin/freebayes
[17:40:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:40:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:40:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:40:54] Found vcfuniq - /usr/local/bin/vcfuniq
[17:40:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:40:54] Found gzip - /bin/gzip
[17:40:54] Found vt - /usr/local/bin/vt
[17:40:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:40:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:40:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:40:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:40:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:40:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:40:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:40:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:37:44] This is snippy 4.6.0Show full stderr[17:37:44] This is snippy 4.6.0
[17:37:44] Written by Torsten Seemann
[17:37:44] Obtained from https://github.com/tseemann/snippy
[17:37:44] Detected operating system: linux
[17:37:44] Enabling bundled linux tools.
[17:37:44] Found bwa - /usr/local/bin/bwa
[17:37:44] Found bcftools - /usr/local/bin/bcftools
[17:37:44] Found samtools - /usr/local/bin/samtools
[17:37:44] Found java - /usr/local/bin/java
[17:37:44] Found snpEff - /usr/local/bin/snpEff
[17:37:44] Found samclip - /usr/local/bin/samclip
[17:37:44] Found seqtk - /usr/local/bin/seqtk
[17:37:44] Found parallel - /usr/local/bin/parallel
[17:37:44] Found freebayes - /usr/local/bin/freebayes
[17:37:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:37:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:37:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:37:45] Found vcfuniq - /usr/local/bin/vcfuniq
[17:37:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:37:45] Found gzip - /bin/gzip
[17:37:45] Found vt - /usr/local/bin/vt
[17:37:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:37:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:37:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:37:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:37:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:37:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:37:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:37:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:38:48] This is snippy 4.6.0Show full stderr[17:38:48] This is snippy 4.6.0
[17:38:48] Written by Torsten Seemann
[17:38:48] Obtained from https://github.com/tseemann/snippy
[17:38:48] Detected operating system: linux
[17:38:48] Enabling bundled linux tools.
[17:38:48] Found bwa - /usr/local/bin/bwa
[17:38:48] Found bcftools - /usr/local/bin/bcftools
[17:38:48] Found samtools - /usr/local/bin/samtools
[17:38:48] Found java - /usr/local/bin/java
[17:38:48] Found snpEff - /usr/local/bin/snpEff
[17:38:48] Found samclip - /usr/local/bin/samclip
[17:38:48] Found seqtk - /usr/local/bin/seqtk
[17:38:48] Found parallel - /usr/local/bin/parallel
[17:38:48] Found freebayes - /usr/local/bin/freebayes
[17:38:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:38:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:38:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:38:48] Found vcfuniq - /usr/local/bin/vcfuniq
[17:38:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:38:48] Found gzip - /bin/gzip
[17:38:48] Found vt - /usr/local/bin/vt
[17:38:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:38:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:38:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:38:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:38:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:38:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:38:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:38:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:39:21] This is snippy 4.6.0Show full stderr[17:39:21] This is snippy 4.6.0
[17:39:21] Written by Torsten Seemann
[17:39:21] Obtained from https://github.com/tseemann/snippy
[17:39:21] Detected operating system: linux
[17:39:21] Enabling bundled linux tools.
[17:39:21] Found bwa - /usr/local/bin/bwa
[17:39:21] Found bcftools - /usr/local/bin/bcftools
[17:39:21] Found samtools - /usr/local/bin/samtools
[17:39:21] Found java - /usr/local/bin/java
[17:39:21] Found snpEff - /usr/local/bin/snpEff
[17:39:21] Found samclip - /usr/local/bin/samclip
[17:39:21] Found seqtk - /usr/local/bin/seqtk
[17:39:21] Found parallel - /usr/local/bin/parallel
[17:39:21] Found freebayes - /usr/local/bin/freebayes
[17:39:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:39:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:39:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:39:21] Found vcfuniq - /usr/local/bin/vcfuniq
[17:39:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:39:21] Found gzip - /bin/gzip
[17:39:21] Found vt - /usr/local/bin/vt
[17:39:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:39:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:39:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:39:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:39:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:39:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:39:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:39:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:43:07] This is snippy 4.6.0Show full stderr[17:43:07] This is snippy 4.6.0
[17:43:07] Written by Torsten Seemann
[17:43:07] Obtained from https://github.com/tseemann/snippy
[17:43:07] Detected operating system: linux
[17:43:07] Enabling bundled linux tools.
[17:43:07] Found bwa - /usr/local/bin/bwa
[17:43:07] Found bcftools - /usr/local/bin/bcftools
[17:43:08] Found samtools - /usr/local/bin/samtools
[17:43:08] Found java - /usr/local/bin/java
[17:43:08] Found snpEff - /usr/local/bin/snpEff
[17:43:08] Found samclip - /usr/local/bin/samclip
[17:43:08] Found seqtk - /usr/local/bin/seqtk
[17:43:08] Found parallel - /usr/local/bin/parallel
[17:43:08] Found freebayes - /usr/local/bin/freebayes
[17:43:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:43:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:43:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:43:08] Found vcfuniq - /usr/local/bin/vcfuniq
[17:43:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:43:08] Found gzip - /bin/gzip
[17:43:08] Found vt - /usr/local/bin/vt
[17:43:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:43:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:43:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:43:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:43:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:43:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:43:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:43:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:43:14] This is snippy 4.6.0Show full stderr[17:43:14] This is snippy 4.6.0
[17:43:14] Written by Torsten Seemann
[17:43:14] Obtained from https://github.com/tseemann/snippy
[17:43:14] Detected operating system: linux
[17:43:14] Enabling bundled linux tools.
[17:43:14] Found bwa - /usr/local/bin/bwa
[17:43:14] Found bcftools - /usr/local/bin/bcftools
[17:43:14] Found samtools - /usr/local/bin/samtools
[17:43:14] Found java - /usr/local/bin/java
[17:43:14] Found snpEff - /usr/local/bin/snpEff
[17:43:14] Found samclip - /usr/local/bin/samclip
[17:43:14] Found seqtk - /usr/local/bin/seqtk
[17:43:14] Found parallel - /usr/local/bin/parallel
[17:43:14] Found freebayes - /usr/local/bin/freebayes
[17:43:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:43:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:43:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:43:14] Found vcfuniq - /usr/local/bin/vcfuniq
[17:43:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:43:14] Found gzip - /bin/gzip
[17:43:14] Found vt - /usr/local/bin/vt
[17:43:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:43:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:43:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:43:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:43:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:43:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:43:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:43:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:43:43] This is snippy 4.6.0Show full stderr[17:43:43] This is snippy 4.6.0
[17:43:43] Written by Torsten Seemann
[17:43:43] Obtained from https://github.com/tseemann/snippy
[17:43:43] Detected operating system: linux
[17:43:43] Enabling bundled linux tools.
[17:43:43] Found bwa - /usr/local/bin/bwa
[17:43:44] Found bcftools - /usr/local/bin/bcftools
[17:43:44] Found samtools - /usr/local/bin/samtools
[17:43:44] Found java - /usr/local/bin/java
[17:43:44] Found snpEff - /usr/local/bin/snpEff
[17:43:44] Found samclip - /usr/local/bin/samclip
[17:43:44] Found seqtk - /usr/local/bin/seqtk
[17:43:44] Found parallel - /usr/local/bin/parallel
[17:43:44] Found freebayes - /usr/local/bin/freebayes
[17:43:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:43:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:43:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:43:44] Found vcfuniq - /usr/local/bin/vcfuniq
[17:43:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:43:44] Found gzip - /bin/gzip
[17:43:44] Found vt - /usr/local/bin/vt
[17:43:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:43:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:43:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:43:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:43:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:43:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:43:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:43:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:44:32] This is snippy 4.6.0Show full stderr[17:44:32] This is snippy 4.6.0
[17:44:32] Written by Torsten Seemann
[17:44:32] Obtained from https://github.com/tseemann/snippy
[17:44:32] Detected operating system: linux
[17:44:32] Enabling bundled linux tools.
[17:44:32] Found bwa - /usr/local/bin/bwa
[17:44:32] Found bcftools - /usr/local/bin/bcftools
[17:44:33] Found samtools - /usr/local/bin/samtools
[17:44:33] Found java - /usr/local/bin/java
[17:44:33] Found snpEff - /usr/local/bin/snpEff
[17:44:33] Found samclip - /usr/local/bin/samclip
[17:44:33] Found seqtk - /usr/local/bin/seqtk
[17:44:33] Found parallel - /usr/local/bin/parallel
[17:44:33] Found freebayes - /usr/local/bin/freebayes
[17:44:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:44:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:44:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:44:33] Found vcfuniq - /usr/local/bin/vcfuniq
[17:44:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:44:33] Found gzip - /bin/gzip
[17:44:33] Found vt - /usr/local/bin/vt
[17:44:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:44:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:44:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:44:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:44:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:44:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:44:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:44:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:44:42] This is snippy 4.6.0Show full stderr[17:44:42] This is snippy 4.6.0
[17:44:42] Written by Torsten Seemann
[17:44:42] Obtained from https://github.com/tseemann/snippy
[17:44:42] Detected operating system: linux
[17:44:42] Enabling bundled linux tools.
[17:44:42] Found bwa - /usr/local/bin/bwa
[17:44:42] Found bcftools - /usr/local/bin/bcftools
[17:44:42] Found samtools - /usr/local/bin/samtools
[17:44:42] Found java - /usr/local/bin/java
[17:44:42] Found snpEff - /usr/local/bin/snpEff
[17:44:42] Found samclip - /usr/local/bin/samclip
[17:44:42] Found seqtk - /usr/local/bin/seqtk
[17:44:42] Found parallel - /usr/local/bin/parallel
[17:44:42] Found freebayes - /usr/local/bin/freebayes
[17:44:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:44:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:44:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:44:42] Found vcfuniq - /usr/local/bin/vcfuniq
[17:44:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:44:42] Found gzip - /bin/gzip
[17:44:42] Found vt - /usr/local/bin/vt
[17:44:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:44:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:44:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:44:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:44:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:44:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:44:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:44:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:45:09] This is snippy 4.6.0Show full stderr[17:45:09] This is snippy 4.6.0
[17:45:09] Written by Torsten Seemann
[17:45:09] Obtained from https://github.com/tseemann/snippy
[17:45:09] Detected operating system: linux
[17:45:09] Enabling bundled linux tools.
[17:45:09] Found bwa - /usr/local/bin/bwa
[17:45:09] Found bcftools - /usr/local/bin/bcftools
[17:45:09] Found samtools - /usr/local/bin/samtools
[17:45:09] Found java - /usr/local/bin/java
[17:45:09] Found snpEff - /usr/local/bin/snpEff
[17:45:09] Found samclip - /usr/local/bin/samclip
[17:45:09] Found seqtk - /usr/local/bin/seqtk
[17:45:09] Found parallel - /usr/local/bin/parallel
[17:45:09] Found freebayes - /usr/local/bin/freebayes
[17:45:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:45:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:45:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:45:09] Found vcfuniq - /usr/local/bin/vcfuniq
[17:45:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:45:09] Found gzip - /bin/gzip
[17:45:09] Found vt - /usr/local/bin/vt
[17:45:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:45:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:45:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:45:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:45:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:45:12] This is snippy 4.6.0Show full stderr[17:45:12] This is snippy 4.6.0
[17:45:12] Written by Torsten Seemann
[17:45:12] Obtained from https://github.com/tseemann/snippy
[17:45:12] Detected operating system: linux
[17:45:12] Enabling bundled linux tools.
[17:45:12] Found bwa - /usr/local/bin/bwa
[17:45:12] Found bcftools - /usr/local/bin/bcftools
[17:45:12] Found samtools - /usr/local/bin/samtools
[17:45:13] Found java - /usr/local/bin/java
[17:45:13] Found snpEff - /usr/local/bin/snpEff
[17:45:13] Found samclip - /usr/local/bin/samclip
[17:45:13] Found seqtk - /usr/local/bin/seqtk
[17:45:13] Found parallel - /usr/local/bin/parallel
[17:45:13] Found freebayes - /usr/local/bin/freebayes
[17:45:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:45:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:45:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:45:13] Found vcfuniq - /usr/local/bin/vcfuniq
[17:45:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:45:13] Found gzip - /bin/gzip
[17:45:13] Found vt - /usr/local/bin/vt
[17:45:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:45:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:45:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:45:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:45:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:37:51] This is snippy 4.6.0Show full stderr[17:37:51] This is snippy 4.6.0
[17:37:51] Written by Torsten Seemann
[17:37:51] Obtained from https://github.com/tseemann/snippy
[17:37:51] Detected operating system: linux
[17:37:51] Enabling bundled linux tools.
[17:37:51] Found bwa - /usr/local/bin/bwa
[17:37:51] Found bcftools - /usr/local/bin/bcftools
[17:37:51] Found samtools - /usr/local/bin/samtools
[17:37:51] Found java - /usr/local/bin/java
[17:37:51] Found snpEff - /usr/local/bin/snpEff
[17:37:51] Found samclip - /usr/local/bin/samclip
[17:37:51] Found seqtk - /usr/local/bin/seqtk
[17:37:51] Found parallel - /usr/local/bin/parallel
[17:37:51] Found freebayes - /usr/local/bin/freebayes
[17:37:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:37:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:37:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:37:51] Found vcfuniq - /usr/local/bin/vcfuniq
[17:37:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:37:51] Found gzip - /bin/gzip
[17:37:51] Found vt - /usr/local/bin/vt
[17:37:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:37:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:37:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:37:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:37:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:37:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:37:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:37:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:39:03] This is snippy 4.6.0Show full stderr[17:39:03] This is snippy 4.6.0
[17:39:03] Written by Torsten Seemann
[17:39:03] Obtained from https://github.com/tseemann/snippy
[17:39:03] Detected operating system: linux
[17:39:03] Enabling bundled linux tools.
[17:39:03] Found bwa - /usr/local/bin/bwa
[17:39:03] Found bcftools - /usr/local/bin/bcftools
[17:39:03] Found samtools - /usr/local/bin/samtools
[17:39:03] Found java - /usr/local/bin/java
[17:39:03] Found snpEff - /usr/local/bin/snpEff
[17:39:03] Found samclip - /usr/local/bin/samclip
[17:39:03] Found seqtk - /usr/local/bin/seqtk
[17:39:03] Found parallel - /usr/local/bin/parallel
[17:39:03] Found freebayes - /usr/local/bin/freebayes
[17:39:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:39:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:39:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:39:03] Found vcfuniq - /usr/local/bin/vcfuniq
[17:39:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:39:03] Found gzip - /bin/gzip
[17:39:03] Found vt - /usr/local/bin/vt
[17:39:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:39:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:39:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:39:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:39:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:39:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:39:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:39:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:39:45] This is snippy 4.6.0Show full stderr[17:39:45] This is snippy 4.6.0
[17:39:45] Written by Torsten Seemann
[17:39:45] Obtained from https://github.com/tseemann/snippy
[17:39:45] Detected operating system: linux
[17:39:45] Enabling bundled linux tools.
[17:39:45] Found bwa - /usr/local/bin/bwa
[17:39:45] Found bcftools - /usr/local/bin/bcftools
[17:39:45] Found samtools - /usr/local/bin/samtools
[17:39:45] Found java - /usr/local/bin/java
[17:39:45] Found snpEff - /usr/local/bin/snpEff
[17:39:45] Found samclip - /usr/local/bin/samclip
[17:39:45] Found seqtk - /usr/local/bin/seqtk
[17:39:45] Found parallel - /usr/local/bin/parallel
[17:39:45] Found freebayes - /usr/local/bin/freebayes
[17:39:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:39:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:39:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:39:45] Found vcfuniq - /usr/local/bin/vcfuniq
[17:39:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:39:45] Found gzip - /bin/gzip
[17:39:45] Found vt - /usr/local/bin/vt
[17:39:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:39:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:39:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:39:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:39:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:39:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:39:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:39:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:40:04] This is snippy 4.6.0Show full stderr[17:40:04] This is snippy 4.6.0
[17:40:04] Written by Torsten Seemann
[17:40:04] Obtained from https://github.com/tseemann/snippy
[17:40:04] Detected operating system: linux
[17:40:04] Enabling bundled linux tools.
[17:40:04] Found bwa - /usr/local/bin/bwa
[17:40:04] Found bcftools - /usr/local/bin/bcftools
[17:40:04] Found samtools - /usr/local/bin/samtools
[17:40:04] Found java - /usr/local/bin/java
[17:40:04] Found snpEff - /usr/local/bin/snpEff
[17:40:04] Found samclip - /usr/local/bin/samclip
[17:40:04] Found seqtk - /usr/local/bin/seqtk
[17:40:04] Found parallel - /usr/local/bin/parallel
[17:40:04] Found freebayes - /usr/local/bin/freebayes
[17:40:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:40:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:40:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:40:04] Found vcfuniq - /usr/local/bin/vcfuniq
[17:40:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:40:04] Found gzip - /bin/gzip
[17:40:04] Found vt - /usr/local/bin/vt
[17:40:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:40:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:40:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:40:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:40:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:40:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:40:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:40:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:40:12] This is snippy 4.6.0Show full stderr[17:40:12] This is snippy 4.6.0
[17:40:12] Written by Torsten Seemann
[17:40:12] Obtained from https://github.com/tseemann/snippy
[17:40:12] Detected operating system: linux
[17:40:12] Enabling bundled linux tools.
[17:40:12] Found bwa - /usr/local/bin/bwa
[17:40:12] Found bcftools - /usr/local/bin/bcftools
[17:40:12] Found samtools - /usr/local/bin/samtools
[17:40:12] Found java - /usr/local/bin/java
[17:40:12] Found snpEff - /usr/local/bin/snpEff
[17:40:12] Found samclip - /usr/local/bin/samclip
[17:40:12] Found seqtk - /usr/local/bin/seqtk
[17:40:12] Found parallel - /usr/local/bin/parallel
[17:40:12] Found freebayes - /usr/local/bin/freebayes
[17:40:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:40:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:40:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:40:12] Found vcfuniq - /usr/local/bin/vcfuniq
[17:40:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:40:12] Found gzip - /bin/gzip
[17:40:12] Found vt - /usr/local/bin/vt
[17:40:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:40:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:40:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:40:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:40:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:40:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:40:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:40:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:41:15] This is snippy 4.6.0Show full stderr[17:41:15] This is snippy 4.6.0
[17:41:15] Written by Torsten Seemann
[17:41:15] Obtained from https://github.com/tseemann/snippy
[17:41:15] Detected operating system: linux
[17:41:15] Enabling bundled linux tools.
[17:41:15] Found bwa - /usr/local/bin/bwa
[17:41:15] Found bcftools - /usr/local/bin/bcftools
[17:41:15] Found samtools - /usr/local/bin/samtools
[17:41:15] Found java - /usr/local/bin/java
[17:41:15] Found snpEff - /usr/local/bin/snpEff
[17:41:15] Found samclip - /usr/local/bin/samclip
[17:41:15] Found seqtk - /usr/local/bin/seqtk
[17:41:15] Found parallel - /usr/local/bin/parallel
[17:41:15] Found freebayes - /usr/local/bin/freebayes
[17:41:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:41:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:41:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:41:16] Found vcfuniq - /usr/local/bin/vcfuniq
[17:41:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:41:16] Found gzip - /bin/gzip
[17:41:16] Found vt - /usr/local/bin/vt
[17:41:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:41:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:41:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:41:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:41:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:41:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:41:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:41:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:41:48] This is snippy 4.6.0Show full stderr[17:41:48] This is snippy 4.6.0
[17:41:48] Written by Torsten Seemann
[17:41:48] Obtained from https://github.com/tseemann/snippy
[17:41:48] Detected operating system: linux
[17:41:48] Enabling bundled linux tools.
[17:41:48] Found bwa - /usr/local/bin/bwa
[17:41:48] Found bcftools - /usr/local/bin/bcftools
[17:41:48] Found samtools - /usr/local/bin/samtools
[17:41:48] Found java - /usr/local/bin/java
[17:41:48] Found snpEff - /usr/local/bin/snpEff
[17:41:48] Found samclip - /usr/local/bin/samclip
[17:41:48] Found seqtk - /usr/local/bin/seqtk
[17:41:48] Found parallel - /usr/local/bin/parallel
[17:41:48] Found freebayes - /usr/local/bin/freebayes
[17:41:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:41:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:41:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:41:48] Found vcfuniq - /usr/local/bin/vcfuniq
[17:41:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:41:48] Found gzip - /bin/gzip
[17:41:48] Found vt - /usr/local/bin/vt
[17:41:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:41:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:41:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:41:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:41:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:41:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:41:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:41:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:41:53] This is snippy 4.6.0Show full stderr[17:41:53] This is snippy 4.6.0
[17:41:53] Written by Torsten Seemann
[17:41:53] Obtained from https://github.com/tseemann/snippy
[17:41:53] Detected operating system: linux
[17:41:53] Enabling bundled linux tools.
[17:41:53] Found bwa - /usr/local/bin/bwa
[17:41:53] Found bcftools - /usr/local/bin/bcftools
[17:41:53] Found samtools - /usr/local/bin/samtools
[17:41:53] Found java - /usr/local/bin/java
[17:41:53] Found snpEff - /usr/local/bin/snpEff
[17:41:53] Found samclip - /usr/local/bin/samclip
[17:41:53] Found seqtk - /usr/local/bin/seqtk
[17:41:53] Found parallel - /usr/local/bin/parallel
[17:41:53] Found freebayes - /usr/local/bin/freebayes
[17:41:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:41:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:41:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:41:53] Found vcfuniq - /usr/local/bin/vcfuniq
[17:41:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:41:53] Found gzip - /bin/gzip
[17:41:53] Found vt - /usr/local/bin/vt
[17:41:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:41:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:41:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:41:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:41:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:41:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:41:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:41:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:42:19] This is snippy 4.6.0Show full stderr[17:42:19] This is snippy 4.6.0
[17:42:19] Written by Torsten Seemann
[17:42:19] Obtained from https://github.com/tseemann/snippy
[17:42:19] Detected operating system: linux
[17:42:19] Enabling bundled linux tools.
[17:42:19] Found bwa - /usr/local/bin/bwa
[17:42:19] Found bcftools - /usr/local/bin/bcftools
[17:42:19] Found samtools - /usr/local/bin/samtools
[17:42:19] Found java - /usr/local/bin/java
[17:42:19] Found snpEff - /usr/local/bin/snpEff
[17:42:19] Found samclip - /usr/local/bin/samclip
[17:42:19] Found seqtk - /usr/local/bin/seqtk
[17:42:19] Found parallel - /usr/local/bin/parallel
[17:42:19] Found freebayes - /usr/local/bin/freebayes
[17:42:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:42:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:42:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:42:19] Found vcfuniq - /usr/local/bin/vcfuniq
[17:42:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:42:19] Found gzip - /bin/gzip
[17:42:19] Found vt - /usr/local/bin/vt
[17:42:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:42:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:42:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:42:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:42:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:42:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:42:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:42:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:38:01] This is snippy 4.6.0Show full stderr[17:38:01] This is snippy 4.6.0
[17:38:01] Written by Torsten Seemann
[17:38:01] Obtained from https://github.com/tseemann/snippy
[17:38:01] Detected operating system: linux
[17:38:01] Enabling bundled linux tools.
[17:38:01] Found bwa - /usr/local/bin/bwa
[17:38:01] Found bcftools - /usr/local/bin/bcftools
[17:38:01] Found samtools - /usr/local/bin/samtools
[17:38:01] Found java - /usr/local/bin/java
[17:38:01] Found snpEff - /usr/local/bin/snpEff
[17:38:01] Found samclip - /usr/local/bin/samclip
[17:38:01] Found seqtk - /usr/local/bin/seqtk
[17:38:01] Found parallel - /usr/local/bin/parallel
[17:38:01] Found freebayes - /usr/local/bin/freebayes
[17:38:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:38:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:38:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:38:01] Found vcfuniq - /usr/local/bin/vcfuniq
[17:38:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:38:01] Found gzip - /bin/gzip
[17:38:01] Found vt - /usr/local/bin/vt
[17:38:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:38:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:38:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:38:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:38:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:38:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:38:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:38:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:39:30] This is snippy 4.6.0Show full stderr[17:39:30] This is snippy 4.6.0
[17:39:30] Written by Torsten Seemann
[17:39:30] Obtained from https://github.com/tseemann/snippy
[17:39:30] Detected operating system: linux
[17:39:30] Enabling bundled linux tools.
[17:39:30] Found bwa - /usr/local/bin/bwa
[17:39:30] Found bcftools - /usr/local/bin/bcftools
[17:39:30] Found samtools - /usr/local/bin/samtools
[17:39:31] Found java - /usr/local/bin/java
[17:39:31] Found snpEff - /usr/local/bin/snpEff
[17:39:31] Found samclip - /usr/local/bin/samclip
[17:39:31] Found seqtk - /usr/local/bin/seqtk
[17:39:31] Found parallel - /usr/local/bin/parallel
[17:39:31] Found freebayes - /usr/local/bin/freebayes
[17:39:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:39:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:39:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:39:31] Found vcfuniq - /usr/local/bin/vcfuniq
[17:39:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:39:31] Found gzip - /bin/gzip
[17:39:31] Found vt - /usr/local/bin/vt
[17:39:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:39:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:39:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:39:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:39:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:39:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:39:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:39:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:39:24] This is snippy 4.6.0Show full stderr[17:39:24] This is snippy 4.6.0
[17:39:24] Written by Torsten Seemann
[17:39:24] Obtained from https://github.com/tseemann/snippy
[17:39:24] Detected operating system: linux
[17:39:24] Enabling bundled linux tools.
[17:39:24] Found bwa - /usr/local/bin/bwa
[17:39:24] Found bcftools - /usr/local/bin/bcftools
[17:39:24] Found samtools - /usr/local/bin/samtools
[17:39:24] Found java - /usr/local/bin/java
[17:39:24] Found snpEff - /usr/local/bin/snpEff
[17:39:24] Found samclip - /usr/local/bin/samclip
[17:39:24] Found seqtk - /usr/local/bin/seqtk
[17:39:24] Found parallel - /usr/local/bin/parallel
[17:39:24] Found freebayes - /usr/local/bin/freebayes
[17:39:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:39:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:39:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:39:24] Found vcfuniq - /usr/local/bin/vcfuniq
[17:39:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:39:24] Found gzip - /bin/gzip
[17:39:24] Found vt - /usr/local/bin/vt
[17:39:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:39:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:39:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:39:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:39:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:39:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:39:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:39:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:39:39] This is snippy 4.6.0Show full stderr[17:39:39] This is snippy 4.6.0
[17:39:39] Written by Torsten Seemann
[17:39:39] Obtained from https://github.com/tseemann/snippy
[17:39:39] Detected operating system: linux
[17:39:39] Enabling bundled linux tools.
[17:39:39] Found bwa - /usr/local/bin/bwa
[17:39:39] Found bcftools - /usr/local/bin/bcftools
[17:39:39] Found samtools - /usr/local/bin/samtools
[17:39:39] Found java - /usr/local/bin/java
[17:39:39] Found snpEff - /usr/local/bin/snpEff
[17:39:39] Found samclip - /usr/local/bin/samclip
[17:39:39] Found seqtk - /usr/local/bin/seqtk
[17:39:39] Found parallel - /usr/local/bin/parallel
[17:39:39] Found freebayes - /usr/local/bin/freebayes
[17:39:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:39:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:39:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:39:39] Found vcfuniq - /usr/local/bin/vcfuniq
[17:39:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:39:39] Found gzip - /bin/gzip
[17:39:39] Found vt - /usr/local/bin/vt
[17:39:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:39:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:39:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:39:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:39:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:39:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:39:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:39:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:40:00] This is snippy 4.6.0Show full stderr[17:40:00] This is snippy 4.6.0
[17:40:00] Written by Torsten Seemann
[17:40:00] Obtained from https://github.com/tseemann/snippy
[17:40:00] Detected operating system: linux
[17:40:00] Enabling bundled linux tools.
[17:40:00] Found bwa - /usr/local/bin/bwa
[17:40:00] Found bcftools - /usr/local/bin/bcftools
[17:40:00] Found samtools - /usr/local/bin/samtools
[17:40:00] Found java - /usr/local/bin/java
[17:40:00] Found snpEff - /usr/local/bin/snpEff
[17:40:00] Found samclip - /usr/local/bin/samclip
[17:40:00] Found seqtk - /usr/local/bin/seqtk
[17:40:00] Found parallel - /usr/local/bin/parallel
[17:40:00] Found freebayes - /usr/local/bin/freebayes
[17:40:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:40:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:40:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:40:00] Found vcfuniq - /usr/local/bin/vcfuniq
[17:40:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:40:00] Found gzip - /bin/gzip
[17:40:00] Found vt - /usr/local/bin/vt
[17:40:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:40:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:40:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:40:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:40:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:40:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:40:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:40:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:40:25] This is snippy 4.6.0Show full stderr[17:40:25] This is snippy 4.6.0
[17:40:25] Written by Torsten Seemann
[17:40:25] Obtained from https://github.com/tseemann/snippy
[17:40:25] Detected operating system: linux
[17:40:25] Enabling bundled linux tools.
[17:40:25] Found bwa - /usr/local/bin/bwa
[17:40:25] Found bcftools - /usr/local/bin/bcftools
[17:40:26] Found samtools - /usr/local/bin/samtools
[17:40:26] Found java - /usr/local/bin/java
[17:40:26] Found snpEff - /usr/local/bin/snpEff
[17:40:26] Found samclip - /usr/local/bin/samclip
[17:40:26] Found seqtk - /usr/local/bin/seqtk
[17:40:26] Found parallel - /usr/local/bin/parallel
[17:40:26] Found freebayes - /usr/local/bin/freebayes
[17:40:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:40:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:40:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:40:26] Found vcfuniq - /usr/local/bin/vcfuniq
[17:40:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:40:26] Found gzip - /bin/gzip
[17:40:26] Found vt - /usr/local/bin/vt
[17:40:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:40:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:40:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:40:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:40:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:40:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:40:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:40:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:40:34] This is snippy 4.6.0Show full stderr[17:40:34] This is snippy 4.6.0
[17:40:34] Written by Torsten Seemann
[17:40:34] Obtained from https://github.com/tseemann/snippy
[17:40:34] Detected operating system: linux
[17:40:34] Enabling bundled linux tools.
[17:40:34] Found bwa - /usr/local/bin/bwa
[17:40:34] Found bcftools - /usr/local/bin/bcftools
[17:40:34] Found samtools - /usr/local/bin/samtools
[17:40:34] Found java - /usr/local/bin/java
[17:40:34] Found snpEff - /usr/local/bin/snpEff
[17:40:34] Found samclip - /usr/local/bin/samclip
[17:40:34] Found seqtk - /usr/local/bin/seqtk
[17:40:34] Found parallel - /usr/local/bin/parallel
[17:40:34] Found freebayes - /usr/local/bin/freebayes
[17:40:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:40:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:40:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:40:35] Found vcfuniq - /usr/local/bin/vcfuniq
[17:40:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:40:35] Found gzip - /bin/gzip
[17:40:35] Found vt - /usr/local/bin/vt
[17:40:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:40:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:40:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:40:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:40:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:40:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:40:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:40:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:40:39] This is snippy 4.6.0Show full stderr[17:40:39] This is snippy 4.6.0
[17:40:39] Written by Torsten Seemann
[17:40:39] Obtained from https://github.com/tseemann/snippy
[17:40:39] Detected operating system: linux
[17:40:39] Enabling bundled linux tools.
[17:40:39] Found bwa - /usr/local/bin/bwa
[17:40:39] Found bcftools - /usr/local/bin/bcftools
[17:40:39] Found samtools - /usr/local/bin/samtools
[17:40:39] Found java - /usr/local/bin/java
[17:40:39] Found snpEff - /usr/local/bin/snpEff
[17:40:39] Found samclip - /usr/local/bin/samclip
[17:40:39] Found seqtk - /usr/local/bin/seqtk
[17:40:39] Found parallel - /usr/local/bin/parallel
[17:40:39] Found freebayes - /usr/local/bin/freebayes
[17:40:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:40:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:40:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:40:39] Found vcfuniq - /usr/local/bin/vcfuniq
[17:40:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:40:39] Found gzip - /bin/gzip
[17:40:39] Found vt - /usr/local/bin/vt
[17:40:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:40:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:40:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:40:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:40:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:40:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:40:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:40:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:41:45] This is snippy 4.6.0Show full stderr[17:41:45] This is snippy 4.6.0
[17:41:45] Written by Torsten Seemann
[17:41:45] Obtained from https://github.com/tseemann/snippy
[17:41:45] Detected operating system: linux
[17:41:45] Enabling bundled linux tools.
[17:41:45] Found bwa - /usr/local/bin/bwa
[17:41:45] Found bcftools - /usr/local/bin/bcftools
[17:41:45] Found samtools - /usr/local/bin/samtools
[17:41:45] Found java - /usr/local/bin/java
[17:41:45] Found snpEff - /usr/local/bin/snpEff
[17:41:45] Found samclip - /usr/local/bin/samclip
[17:41:45] Found seqtk - /usr/local/bin/seqtk
[17:41:45] Found parallel - /usr/local/bin/parallel
[17:41:45] Found freebayes - /usr/local/bin/freebayes
[17:41:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:41:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:41:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:41:45] Found vcfuniq - /usr/local/bin/vcfuniq
[17:41:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:41:45] Found gzip - /bin/gzip
[17:41:45] Found vt - /usr/local/bin/vt
[17:41:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:41:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:41:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:41:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:41:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:41:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:41:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:41:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:41:55] This is snippy 4.6.0Show full stderr[17:41:55] This is snippy 4.6.0
[17:41:55] Written by Torsten Seemann
[17:41:55] Obtained from https://github.com/tseemann/snippy
[17:41:55] Detected operating system: linux
[17:41:55] Enabling bundled linux tools.
[17:41:55] Found bwa - /usr/local/bin/bwa
[17:41:55] Found bcftools - /usr/local/bin/bcftools
[17:41:55] Found samtools - /usr/local/bin/samtools
[17:41:55] Found java - /usr/local/bin/java
[17:41:55] Found snpEff - /usr/local/bin/snpEff
[17:41:55] Found samclip - /usr/local/bin/samclip
[17:41:55] Found seqtk - /usr/local/bin/seqtk
[17:41:55] Found parallel - /usr/local/bin/parallel
[17:41:55] Found freebayes - /usr/local/bin/freebayes
[17:41:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:41:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:41:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:41:55] Found vcfuniq - /usr/local/bin/vcfuniq
[17:41:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:41:56] Found gzip - /bin/gzip
[17:41:56] Found vt - /usr/local/bin/vt
[17:41:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:41:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:41:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:41:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:41:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:41:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:41:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:41:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:41:57] This is snippy 4.6.0Show full stderr[17:41:57] This is snippy 4.6.0
[17:41:57] Written by Torsten Seemann
[17:41:57] Obtained from https://github.com/tseemann/snippy
[17:41:57] Detected operating system: linux
[17:41:57] Enabling bundled linux tools.
[17:41:57] Found bwa - /usr/local/bin/bwa
[17:41:57] Found bcftools - /usr/local/bin/bcftools
[17:41:57] Found samtools - /usr/local/bin/samtools
[17:41:57] Found java - /usr/local/bin/java
[17:41:57] Found snpEff - /usr/local/bin/snpEff
[17:41:57] Found samclip - /usr/local/bin/samclip
[17:41:57] Found seqtk - /usr/local/bin/seqtk
[17:41:57] Found parallel - /usr/local/bin/parallel
[17:41:57] Found freebayes - /usr/local/bin/freebayes
[17:41:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:41:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:41:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:41:57] Found vcfuniq - /usr/local/bin/vcfuniq
[17:41:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:41:57] Found gzip - /bin/gzip
[17:41:57] Found vt - /usr/local/bin/vt
[17:41:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:41:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:41:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:41:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:41:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:41:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:41:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:41:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:42:04] This is snippy 4.6.0Show full stderr[17:42:04] This is snippy 4.6.0
[17:42:04] Written by Torsten Seemann
[17:42:04] Obtained from https://github.com/tseemann/snippy
[17:42:04] Detected operating system: linux
[17:42:04] Enabling bundled linux tools.
[17:42:04] Found bwa - /usr/local/bin/bwa
[17:42:05] Found bcftools - /usr/local/bin/bcftools
[17:42:05] Found samtools - /usr/local/bin/samtools
[17:42:05] Found java - /usr/local/bin/java
[17:42:05] Found snpEff - /usr/local/bin/snpEff
[17:42:05] Found samclip - /usr/local/bin/samclip
[17:42:05] Found seqtk - /usr/local/bin/seqtk
[17:42:05] Found parallel - /usr/local/bin/parallel
[17:42:05] Found freebayes - /usr/local/bin/freebayes
[17:42:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:42:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:42:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:42:05] Found vcfuniq - /usr/local/bin/vcfuniq
[17:42:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:42:05] Found gzip - /bin/gzip
[17:42:05] Found vt - /usr/local/bin/vt
[17:42:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:42:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:42:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:42:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:42:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:42:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:42:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:42:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:42:16] This is snippy 4.6.0Show full stderr[17:42:16] This is snippy 4.6.0
[17:42:16] Written by Torsten Seemann
[17:42:16] Obtained from https://github.com/tseemann/snippy
[17:42:16] Detected operating system: linux
[17:42:16] Enabling bundled linux tools.
[17:42:16] Found bwa - /usr/local/bin/bwa
[17:42:16] Found bcftools - /usr/local/bin/bcftools
[17:42:16] Found samtools - /usr/local/bin/samtools
[17:42:16] Found java - /usr/local/bin/java
[17:42:16] Found snpEff - /usr/local/bin/snpEff
[17:42:16] Found samclip - /usr/local/bin/samclip
[17:42:16] Found seqtk - /usr/local/bin/seqtk
[17:42:16] Found parallel - /usr/local/bin/parallel
[17:42:16] Found freebayes - /usr/local/bin/freebayes
[17:42:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:42:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:42:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:42:16] Found vcfuniq - /usr/local/bin/vcfuniq
[17:42:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:42:16] Found gzip - /bin/gzip
[17:42:16] Found vt - /usr/local/bin/vt
[17:42:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:42:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:42:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:42:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:42:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:42:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:42:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:42:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:42:29] This is snippy 4.6.0Show full stderr[17:42:29] This is snippy 4.6.0
[17:42:29] Written by Torsten Seemann
[17:42:29] Obtained from https://github.com/tseemann/snippy
[17:42:29] Detected operating system: linux
[17:42:29] Enabling bundled linux tools.
[17:42:29] Found bwa - /usr/local/bin/bwa
[17:42:29] Found bcftools - /usr/local/bin/bcftools
[17:42:29] Found samtools - /usr/local/bin/samtools
[17:42:29] Found java - /usr/local/bin/java
[17:42:29] Found snpEff - /usr/local/bin/snpEff
[17:42:29] Found samclip - /usr/local/bin/samclip
[17:42:29] Found seqtk - /usr/local/bin/seqtk
[17:42:29] Found parallel - /usr/local/bin/parallel
[17:42:29] Found freebayes - /usr/local/bin/freebayes
[17:42:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:42:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:42:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:42:29] Found vcfuniq - /usr/local/bin/vcfuniq
[17:42:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:42:30] Found gzip - /bin/gzip
[17:42:30] Found vt - /usr/local/bin/vt
[17:42:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:42:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:42:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:42:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:42:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:42:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:42:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:42:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:43:02] This is snippy 4.6.0Show full stderr[17:43:02] This is snippy 4.6.0
[17:43:02] Written by Torsten Seemann
[17:43:02] Obtained from https://github.com/tseemann/snippy
[17:43:02] Detected operating system: linux
[17:43:02] Enabling bundled linux tools.
[17:43:02] Found bwa - /usr/local/bin/bwa
[17:43:02] Found bcftools - /usr/local/bin/bcftools
[17:43:02] Found samtools - /usr/local/bin/samtools
[17:43:02] Found java - /usr/local/bin/java
[17:43:02] Found snpEff - /usr/local/bin/snpEff
[17:43:02] Found samclip - /usr/local/bin/samclip
[17:43:02] Found seqtk - /usr/local/bin/seqtk
[17:43:02] Found parallel - /usr/local/bin/parallel
[17:43:02] Found freebayes - /usr/local/bin/freebayes
[17:43:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:43:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:43:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:43:02] Found vcfuniq - /usr/local/bin/vcfuniq
[17:43:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:43:03] Found gzip - /bin/gzip
[17:43:03] Found vt - /usr/local/bin/vt
[17:43:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:43:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:43:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:43:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:43:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:43:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:43:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:43:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:44:14] This is snippy 4.6.0Show full stderr[17:44:14] This is snippy 4.6.0
[17:44:14] Written by Torsten Seemann
[17:44:14] Obtained from https://github.com/tseemann/snippy
[17:44:14] Detected operating system: linux
[17:44:14] Enabling bundled linux tools.
[17:44:15] Found bwa - /usr/local/bin/bwa
[17:44:15] Found bcftools - /usr/local/bin/bcftools
[17:44:15] Found samtools - /usr/local/bin/samtools
[17:44:15] Found java - /usr/local/bin/java
[17:44:15] Found snpEff - /usr/local/bin/snpEff
[17:44:15] Found samclip - /usr/local/bin/samclip
[17:44:15] Found seqtk - /usr/local/bin/seqtk
[17:44:15] Found parallel - /usr/local/bin/parallel
[17:44:15] Found freebayes - /usr/local/bin/freebayes
[17:44:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:44:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:44:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:44:15] Found vcfuniq - /usr/local/bin/vcfuniq
[17:44:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:44:15] Found gzip - /bin/gzip
[17:44:15] Found vt - /usr/local/bin/vt
[17:44:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:44:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:44:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:44:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:44:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:44:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:44:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:44:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:44:15] This is snippy 4.6.0Show full stderr[17:44:15] This is snippy 4.6.0
[17:44:15] Written by Torsten Seemann
[17:44:15] Obtained from https://github.com/tseemann/snippy
[17:44:15] Detected operating system: linux
[17:44:15] Enabling bundled linux tools.
[17:44:15] Found bwa - /usr/local/bin/bwa
[17:44:15] Found bcftools - /usr/local/bin/bcftools
[17:44:15] Found samtools - /usr/local/bin/samtools
[17:44:16] Found java - /usr/local/bin/java
[17:44:16] Found snpEff - /usr/local/bin/snpEff
[17:44:16] Found samclip - /usr/local/bin/samclip
[17:44:16] Found seqtk - /usr/local/bin/seqtk
[17:44:16] Found parallel - /usr/local/bin/parallel
[17:44:16] Found freebayes - /usr/local/bin/freebayes
[17:44:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:44:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:44:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:44:16] Found vcfuniq - /usr/local/bin/vcfuniq
[17:44:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:44:16] Found gzip - /bin/gzip
[17:44:16] Found vt - /usr/local/bin/vt
[17:44:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:44:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:44:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:44:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:44:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:44:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:44:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:44:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:44:45] This is snippy 4.6.0Show full stderr[17:44:45] This is snippy 4.6.0
[17:44:45] Written by Torsten Seemann
[17:44:45] Obtained from https://github.com/tseemann/snippy
[17:44:45] Detected operating system: linux
[17:44:45] Enabling bundled linux tools.
[17:44:45] Found bwa - /usr/local/bin/bwa
[17:44:45] Found bcftools - /usr/local/bin/bcftools
[17:44:45] Found samtools - /usr/local/bin/samtools
[17:44:45] Found java - /usr/local/bin/java
[17:44:45] Found snpEff - /usr/local/bin/snpEff
[17:44:45] Found samclip - /usr/local/bin/samclip
[17:44:45] Found seqtk - /usr/local/bin/seqtk
[17:44:45] Found parallel - /usr/local/bin/parallel
[17:44:45] Found freebayes - /usr/local/bin/freebayes
[17:44:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:44:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:44:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:44:45] Found vcfuniq - /usr/local/bin/vcfuniq
[17:44:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:44:45] Found gzip - /bin/gzip
[17:44:45] Found vt - /usr/local/bin/vt
[17:44:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:44:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:44:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:44:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:44:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:44:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:44:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:44:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:44:55] This is snippy 4.6.0Show full stderr[17:44:55] This is snippy 4.6.0
[17:44:55] Written by Torsten Seemann
[17:44:55] Obtained from https://github.com/tseemann/snippy
[17:44:55] Detected operating system: linux
[17:44:55] Enabling bundled linux tools.
[17:44:55] Found bwa - /usr/local/bin/bwa
[17:44:55] Found bcftools - /usr/local/bin/bcftools
[17:44:55] Found samtools - /usr/local/bin/samtools
[17:44:55] Found java - /usr/local/bin/java
[17:44:55] Found snpEff - /usr/local/bin/snpEff
[17:44:55] Found samclip - /usr/local/bin/samclip
[17:44:55] Found seqtk - /usr/local/bin/seqtk
[17:44:55] Found parallel - /usr/local/bin/parallel
[17:44:55] Found freebayes - /usr/local/bin/freebayes
[17:44:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:44:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:44:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:44:55] Found vcfuniq - /usr/local/bin/vcfuniq
[17:44:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:44:55] Found gzip - /bin/gzip
[17:44:55] Found vt - /usr/local/bin/vt
[17:44:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:44:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:44:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:44:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:44:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:44:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:44:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:44:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:49:01] This is snippy 4.6.0Show full stderr[17:49:01] This is snippy 4.6.0
[17:49:01] Written by Torsten Seemann
[17:49:01] Obtained from https://github.com/tseemann/snippy
[17:49:01] Detected operating system: linux
[17:49:01] Enabling bundled linux tools.
[17:49:01] Found bwa - /usr/local/bin/bwa
[17:49:01] Found bcftools - /usr/local/bin/bcftools
[17:49:01] Found samtools - /usr/local/bin/samtools
[17:49:01] Found java - /usr/local/bin/java
[17:49:01] Found snpEff - /usr/local/bin/snpEff
[17:49:01] Found samclip - /usr/local/bin/samclip
[17:49:01] Found seqtk - /usr/local/bin/seqtk
[17:49:01] Found parallel - /usr/local/bin/parallel
[17:49:01] Found freebayes - /usr/local/bin/freebayes
[17:49:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:49:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:49:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:49:01] Found vcfuniq - /usr/local/bin/vcfuniq
[17:49:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:49:01] Found gzip - /bin/gzip
[17:49:01] Found vt - /usr/local/bin/vt
[17:49:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:49:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:49:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:49:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:49:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:49:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:49:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:49:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:55:17] This is snippy 4.6.0Show full stderr[17:55:17] This is snippy 4.6.0
[17:55:17] Written by Torsten Seemann
[17:55:17] Obtained from https://github.com/tseemann/snippy
[17:55:17] Detected operating system: linux
[17:55:17] Enabling bundled linux tools.
[17:55:17] Found bwa - /usr/local/bin/bwa
[17:55:17] Found bcftools - /usr/local/bin/bcftools
[17:55:17] Found samtools - /usr/local/bin/samtools
[17:55:17] Found java - /usr/local/bin/java
[17:55:17] Found snpEff - /usr/local/bin/snpEff
[17:55:17] Found samclip - /usr/local/bin/samclip
[17:55:17] Found seqtk - /usr/local/bin/seqtk
[17:55:17] Found parallel - /usr/local/bin/parallel
[17:55:17] Found freebayes - /usr/local/bin/freebayes
[17:55:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:55:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:55:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:55:17] Found vcfuniq - /usr/local/bin/vcfuniq
[17:55:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:55:17] Found gzip - /bin/gzip
[17:55:17] Found vt - /usr/local/bin/vt
[17:55:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:55:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:55:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:55:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:55:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:55:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:55:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:55:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:45:13] This is snippy 4.6.0Show full stderr[17:45:13] This is snippy 4.6.0
[17:45:13] Written by Torsten Seemann
[17:45:13] Obtained from https://github.com/tseemann/snippy
[17:45:13] Detected operating system: linux
[17:45:13] Enabling bundled linux tools.
[17:45:13] Found bwa - /usr/local/bin/bwa
[17:45:13] Found bcftools - /usr/local/bin/bcftools
[17:45:13] Found samtools - /usr/local/bin/samtools
[17:45:13] Found java - /usr/local/bin/java
[17:45:13] Found snpEff - /usr/local/bin/snpEff
[17:45:13] Found samclip - /usr/local/bin/samclip
[17:45:13] Found seqtk - /usr/local/bin/seqtk
[17:45:13] Found parallel - /usr/local/bin/parallel
[17:45:13] Found freebayes - /usr/local/bin/freebayes
[17:45:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:45:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:45:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:45:13] Found vcfuniq - /usr/local/bin/vcfuniq
[17:45:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:45:13] Found gzip - /bin/gzip
[17:45:13] Found vt - /usr/local/bin/vt
[17:45:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:45:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:45:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:45:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:45:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:45:21] This is snippy 4.6.0Show full stderr[17:45:21] This is snippy 4.6.0
[17:45:21] Written by Torsten Seemann
[17:45:21] Obtained from https://github.com/tseemann/snippy
[17:45:21] Detected operating system: linux
[17:45:21] Enabling bundled linux tools.
[17:45:21] Found bwa - /usr/local/bin/bwa
[17:45:21] Found bcftools - /usr/local/bin/bcftools
[17:45:21] Found samtools - /usr/local/bin/samtools
[17:45:21] Found java - /usr/local/bin/java
[17:45:21] Found snpEff - /usr/local/bin/snpEff
[17:45:21] Found samclip - /usr/local/bin/samclip
[17:45:21] Found seqtk - /usr/local/bin/seqtk
[17:45:21] Found parallel - /usr/local/bin/parallel
[17:45:21] Found freebayes - /usr/local/bin/freebayes
[17:45:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:45:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:45:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:45:21] Found vcfuniq - /usr/local/bin/vcfuniq
[17:45:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:45:21] Found gzip - /bin/gzip
[17:45:21] Found vt - /usr/local/bin/vt
[17:45:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:45:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:45:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:45:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:45:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:45:36] This is snippy 4.6.0Show full stderr[17:45:36] This is snippy 4.6.0
[17:45:36] Written by Torsten Seemann
[17:45:36] Obtained from https://github.com/tseemann/snippy
[17:45:36] Detected operating system: linux
[17:45:36] Enabling bundled linux tools.
[17:45:36] Found bwa - /usr/local/bin/bwa
[17:45:36] Found bcftools - /usr/local/bin/bcftools
[17:45:36] Found samtools - /usr/local/bin/samtools
[17:45:36] Found java - /usr/local/bin/java
[17:45:36] Found snpEff - /usr/local/bin/snpEff
[17:45:36] Found samclip - /usr/local/bin/samclip
[17:45:36] Found seqtk - /usr/local/bin/seqtk
[17:45:36] Found parallel - /usr/local/bin/parallel
[17:45:36] Found freebayes - /usr/local/bin/freebayes
[17:45:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:45:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:45:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:45:36] Found vcfuniq - /usr/local/bin/vcfuniq
[17:45:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:45:36] Found gzip - /bin/gzip
[17:45:36] Found vt - /usr/local/bin/vt
[17:45:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:45:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:45:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:45:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:45:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:45:42] This is snippy 4.6.0Show full stderr[17:45:42] This is snippy 4.6.0
[17:45:42] Written by Torsten Seemann
[17:45:42] Obtained from https://github.com/tseemann/snippy
[17:45:42] Detected operating system: linux
[17:45:42] Enabling bundled linux tools.
[17:45:42] Found bwa - /usr/local/bin/bwa
[17:45:42] Found bcftools - /usr/local/bin/bcftools
[17:45:42] Found samtools - /usr/local/bin/samtools
[17:45:42] Found java - /usr/local/bin/java
[17:45:42] Found snpEff - /usr/local/bin/snpEff
[17:45:42] Found samclip - /usr/local/bin/samclip
[17:45:42] Found seqtk - /usr/local/bin/seqtk
[17:45:42] Found parallel - /usr/local/bin/parallel
[17:45:42] Found freebayes - /usr/local/bin/freebayes
[17:45:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:45:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:45:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:45:42] Found vcfuniq - /usr/local/bin/vcfuniq
[17:45:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:45:42] Found gzip - /bin/gzip
[17:45:42] Found vt - /usr/local/bin/vt
[17:45:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:45:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:45:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:45:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:45:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:45:51] This is snippy 4.6.0Show full stderr[17:45:51] This is snippy 4.6.0
[17:45:51] Written by Torsten Seemann
[17:45:51] Obtained from https://github.com/tseemann/snippy
[17:45:51] Detected operating system: linux
[17:45:51] Enabling bundled linux tools.
[17:45:51] Found bwa - /usr/local/bin/bwa
[17:45:51] Found bcftools - /usr/local/bin/bcftools
[17:45:51] Found samtools - /usr/local/bin/samtools
[17:45:51] Found java - /usr/local/bin/java
[17:45:51] Found snpEff - /usr/local/bin/snpEff
[17:45:51] Found samclip - /usr/local/bin/samclip
[17:45:51] Found seqtk - /usr/local/bin/seqtk
[17:45:51] Found parallel - /usr/local/bin/parallel
[17:45:51] Found freebayes - /usr/local/bin/freebayes
[17:45:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:45:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:45:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:45:51] Found vcfuniq - /usr/local/bin/vcfuniq
[17:45:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:45:51] Found gzip - /bin/gzip
[17:45:51] Found vt - /usr/local/bin/vt
[17:45:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:45:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:45:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:45:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:45:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:46:00] This is snippy 4.6.0Show full stderr[17:46:00] This is snippy 4.6.0
[17:46:00] Written by Torsten Seemann
[17:46:00] Obtained from https://github.com/tseemann/snippy
[17:46:00] Detected operating system: linux
[17:46:00] Enabling bundled linux tools.
[17:46:00] Found bwa - /usr/local/bin/bwa
[17:46:00] Found bcftools - /usr/local/bin/bcftools
[17:46:00] Found samtools - /usr/local/bin/samtools
[17:46:00] Found java - /usr/local/bin/java
[17:46:00] Found snpEff - /usr/local/bin/snpEff
[17:46:00] Found samclip - /usr/local/bin/samclip
[17:46:00] Found seqtk - /usr/local/bin/seqtk
[17:46:00] Found parallel - /usr/local/bin/parallel
[17:46:00] Found freebayes - /usr/local/bin/freebayes
[17:46:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:46:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:46:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:46:00] Found vcfuniq - /usr/local/bin/vcfuniq
[17:46:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:46:00] Found gzip - /bin/gzip
[17:46:00] Found vt - /usr/local/bin/vt
[17:46:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:46:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:46:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:46:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:46:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:46:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:46:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:46:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:46:14] This is snippy 4.6.0Show full stderr[17:46:14] This is snippy 4.6.0
[17:46:14] Written by Torsten Seemann
[17:46:14] Obtained from https://github.com/tseemann/snippy
[17:46:14] Detected operating system: linux
[17:46:14] Enabling bundled linux tools.
[17:46:14] Found bwa - /usr/local/bin/bwa
[17:46:14] Found bcftools - /usr/local/bin/bcftools
[17:46:14] Found samtools - /usr/local/bin/samtools
[17:46:14] Found java - /usr/local/bin/java
[17:46:14] Found snpEff - /usr/local/bin/snpEff
[17:46:14] Found samclip - /usr/local/bin/samclip
[17:46:14] Found seqtk - /usr/local/bin/seqtk
[17:46:14] Found parallel - /usr/local/bin/parallel
[17:46:14] Found freebayes - /usr/local/bin/freebayes
[17:46:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:46:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:46:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:46:14] Found vcfuniq - /usr/local/bin/vcfuniq
[17:46:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:46:14] Found gzip - /bin/gzip
[17:46:14] Found vt - /usr/local/bin/vt
[17:46:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:46:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:46:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:46:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:46:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:46:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:46:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:46:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:46:12] This is snippy 4.6.0Show full stderr[17:46:12] This is snippy 4.6.0
[17:46:12] Written by Torsten Seemann
[17:46:12] Obtained from https://github.com/tseemann/snippy
[17:46:12] Detected operating system: linux
[17:46:12] Enabling bundled linux tools.
[17:46:12] Found bwa - /usr/local/bin/bwa
[17:46:12] Found bcftools - /usr/local/bin/bcftools
[17:46:12] Found samtools - /usr/local/bin/samtools
[17:46:12] Found java - /usr/local/bin/java
[17:46:12] Found snpEff - /usr/local/bin/snpEff
[17:46:12] Found samclip - /usr/local/bin/samclip
[17:46:12] Found seqtk - /usr/local/bin/seqtk
[17:46:12] Found parallel - /usr/local/bin/parallel
[17:46:12] Found freebayes - /usr/local/bin/freebayes
[17:46:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:46:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:46:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:46:12] Found vcfuniq - /usr/local/bin/vcfuniq
[17:46:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:46:12] Found gzip - /bin/gzip
[17:46:12] Found vt - /usr/local/bin/vt
[17:46:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:46:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:46:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:46:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:46:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:46:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:46:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:46:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:46:43] This is snippy 4.6.0Show full stderr[17:46:43] This is snippy 4.6.0
[17:46:43] Written by Torsten Seemann
[17:46:43] Obtained from https://github.com/tseemann/snippy
[17:46:43] Detected operating system: linux
[17:46:43] Enabling bundled linux tools.
[17:46:43] Found bwa - /usr/local/bin/bwa
[17:46:43] Found bcftools - /usr/local/bin/bcftools
[17:46:43] Found samtools - /usr/local/bin/samtools
[17:46:43] Found java - /usr/local/bin/java
[17:46:43] Found snpEff - /usr/local/bin/snpEff
[17:46:43] Found samclip - /usr/local/bin/samclip
[17:46:43] Found seqtk - /usr/local/bin/seqtk
[17:46:43] Found parallel - /usr/local/bin/parallel
[17:46:43] Found freebayes - /usr/local/bin/freebayes
[17:46:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:46:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:46:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:46:43] Found vcfuniq - /usr/local/bin/vcfuniq
[17:46:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:46:44] Found gzip - /bin/gzip
[17:46:44] Found vt - /usr/local/bin/vt
[17:46:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:46:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:46:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:46:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:46:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:46:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:46:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:46:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:46:36] This is snippy 4.6.0Show full stderr[17:46:36] This is snippy 4.6.0
[17:46:36] Written by Torsten Seemann
[17:46:36] Obtained from https://github.com/tseemann/snippy
[17:46:36] Detected operating system: linux
[17:46:36] Enabling bundled linux tools.
[17:46:36] Found bwa - /usr/local/bin/bwa
[17:46:36] Found bcftools - /usr/local/bin/bcftools
[17:46:36] Found samtools - /usr/local/bin/samtools
[17:46:36] Found java - /usr/local/bin/java
[17:46:36] Found snpEff - /usr/local/bin/snpEff
[17:46:36] Found samclip - /usr/local/bin/samclip
[17:46:36] Found seqtk - /usr/local/bin/seqtk
[17:46:36] Found parallel - /usr/local/bin/parallel
[17:46:36] Found freebayes - /usr/local/bin/freebayes
[17:46:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:46:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:46:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:46:36] Found vcfuniq - /usr/local/bin/vcfuniq
[17:46:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:46:36] Found gzip - /bin/gzip
[17:46:36] Found vt - /usr/local/bin/vt
[17:46:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:46:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:46:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:46:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:46:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:46:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:46:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:46:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:46:42] This is snippy 4.6.0Show full stderr[17:46:42] This is snippy 4.6.0
[17:46:42] Written by Torsten Seemann
[17:46:42] Obtained from https://github.com/tseemann/snippy
[17:46:42] Detected operating system: linux
[17:46:42] Enabling bundled linux tools.
[17:46:42] Found bwa - /usr/local/bin/bwa
[17:46:42] Found bcftools - /usr/local/bin/bcftools
[17:46:42] Found samtools - /usr/local/bin/samtools
[17:46:42] Found java - /usr/local/bin/java
[17:46:42] Found snpEff - /usr/local/bin/snpEff
[17:46:42] Found samclip - /usr/local/bin/samclip
[17:46:42] Found seqtk - /usr/local/bin/seqtk
[17:46:42] Found parallel - /usr/local/bin/parallel
[17:46:42] Found freebayes - /usr/local/bin/freebayes
[17:46:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:46:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:46:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:46:42] Found vcfuniq - /usr/local/bin/vcfuniq
[17:46:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:46:42] Found gzip - /bin/gzip
[17:46:42] Found vt - /usr/local/bin/vt
[17:46:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:46:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:46:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:46:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:46:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:46:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:46:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:46:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:46:51] This is snippy 4.6.0Show full stderr[17:46:51] This is snippy 4.6.0
[17:46:51] Written by Torsten Seemann
[17:46:51] Obtained from https://github.com/tseemann/snippy
[17:46:51] Detected operating system: linux
[17:46:51] Enabling bundled linux tools.
[17:46:51] Found bwa - /usr/local/bin/bwa
[17:46:51] Found bcftools - /usr/local/bin/bcftools
[17:46:51] Found samtools - /usr/local/bin/samtools
[17:46:51] Found java - /usr/local/bin/java
[17:46:51] Found snpEff - /usr/local/bin/snpEff
[17:46:51] Found samclip - /usr/local/bin/samclip
[17:46:51] Found seqtk - /usr/local/bin/seqtk
[17:46:51] Found parallel - /usr/local/bin/parallel
[17:46:51] Found freebayes - /usr/local/bin/freebayes
[17:46:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:46:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:46:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:46:51] Found vcfuniq - /usr/local/bin/vcfuniq
[17:46:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:46:51] Found gzip - /bin/gzip
[17:46:51] Found vt - /usr/local/bin/vt
[17:46:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:46:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:46:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:46:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:46:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:46:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:46:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:46:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:46:59] This is snippy 4.6.0Show full stderr[17:46:59] This is snippy 4.6.0
[17:46:59] Written by Torsten Seemann
[17:46:59] Obtained from https://github.com/tseemann/snippy
[17:46:59] Detected operating system: linux
[17:46:59] Enabling bundled linux tools.
[17:46:59] Found bwa - /usr/local/bin/bwa
[17:46:59] Found bcftools - /usr/local/bin/bcftools
[17:46:59] Found samtools - /usr/local/bin/samtools
[17:46:59] Found java - /usr/local/bin/java
[17:46:59] Found snpEff - /usr/local/bin/snpEff
[17:46:59] Found samclip - /usr/local/bin/samclip
[17:46:59] Found seqtk - /usr/local/bin/seqtk
[17:46:59] Found parallel - /usr/local/bin/parallel
[17:46:59] Found freebayes - /usr/local/bin/freebayes
[17:46:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:46:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:46:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:46:59] Found vcfuniq - /usr/local/bin/vcfuniq
[17:46:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:46:59] Found gzip - /bin/gzip
[17:46:59] Found vt - /usr/local/bin/vt
[17:46:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:46:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:46:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:46:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:46:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:47:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:47:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:47:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:47:13] This is snippy 4.6.0Show full stderr[17:47:13] This is snippy 4.6.0
[17:47:13] Written by Torsten Seemann
[17:47:13] Obtained from https://github.com/tseemann/snippy
[17:47:13] Detected operating system: linux
[17:47:13] Enabling bundled linux tools.
[17:47:13] Found bwa - /usr/local/bin/bwa
[17:47:13] Found bcftools - /usr/local/bin/bcftools
[17:47:13] Found samtools - /usr/local/bin/samtools
[17:47:13] Found java - /usr/local/bin/java
[17:47:13] Found snpEff - /usr/local/bin/snpEff
[17:47:13] Found samclip - /usr/local/bin/samclip
[17:47:13] Found seqtk - /usr/local/bin/seqtk
[17:47:13] Found parallel - /usr/local/bin/parallel
[17:47:13] Found freebayes - /usr/local/bin/freebayes
[17:47:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:47:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:47:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:47:13] Found vcfuniq - /usr/local/bin/vcfuniq
[17:47:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:47:13] Found gzip - /bin/gzip
[17:47:13] Found vt - /usr/local/bin/vt
[17:47:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:47:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:47:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:47:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:47:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:47:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:47:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:47:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:47:20] This is snippy 4.6.0Show full stderr[17:47:20] This is snippy 4.6.0
[17:47:20] Written by Torsten Seemann
[17:47:20] Obtained from https://github.com/tseemann/snippy
[17:47:20] Detected operating system: linux
[17:47:20] Enabling bundled linux tools.
[17:47:20] Found bwa - /usr/local/bin/bwa
[17:47:20] Found bcftools - /usr/local/bin/bcftools
[17:47:20] Found samtools - /usr/local/bin/samtools
[17:47:20] Found java - /usr/local/bin/java
[17:47:20] Found snpEff - /usr/local/bin/snpEff
[17:47:20] Found samclip - /usr/local/bin/samclip
[17:47:20] Found seqtk - /usr/local/bin/seqtk
[17:47:20] Found parallel - /usr/local/bin/parallel
[17:47:20] Found freebayes - /usr/local/bin/freebayes
[17:47:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:47:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:47:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:47:20] Found vcfuniq - /usr/local/bin/vcfuniq
[17:47:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:47:20] Found gzip - /bin/gzip
[17:47:20] Found vt - /usr/local/bin/vt
[17:47:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:47:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:47:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:47:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:47:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:47:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:47:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:47:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:47:24] This is snippy 4.6.0Show full stderr[17:47:24] This is snippy 4.6.0
[17:47:24] Written by Torsten Seemann
[17:47:24] Obtained from https://github.com/tseemann/snippy
[17:47:24] Detected operating system: linux
[17:47:24] Enabling bundled linux tools.
[17:47:24] Found bwa - /usr/local/bin/bwa
[17:47:24] Found bcftools - /usr/local/bin/bcftools
[17:47:24] Found samtools - /usr/local/bin/samtools
[17:47:24] Found java - /usr/local/bin/java
[17:47:24] Found snpEff - /usr/local/bin/snpEff
[17:47:24] Found samclip - /usr/local/bin/samclip
[17:47:24] Found seqtk - /usr/local/bin/seqtk
[17:47:24] Found parallel - /usr/local/bin/parallel
[17:47:24] Found freebayes - /usr/local/bin/freebayes
[17:47:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:47:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:47:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:47:24] Found vcfuniq - /usr/local/bin/vcfuniq
[17:47:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:47:24] Found gzip - /bin/gzip
[17:47:24] Found vt - /usr/local/bin/vt
[17:47:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:47:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:47:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:47:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:47:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:47:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:47:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:47:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:42:58] This is snippy 4.6.0Show full stderr[17:42:58] This is snippy 4.6.0
[17:42:58] Written by Torsten Seemann
[17:42:58] Obtained from https://github.com/tseemann/snippy
[17:42:58] Detected operating system: linux
[17:42:58] Enabling bundled linux tools.
[17:42:58] Found bwa - /usr/local/bin/bwa
[17:42:58] Found bcftools - /usr/local/bin/bcftools
[17:42:58] Found samtools - /usr/local/bin/samtools
[17:42:58] Found java - /usr/local/bin/java
[17:42:58] Found snpEff - /usr/local/bin/snpEff
[17:42:58] Found samclip - /usr/local/bin/samclip
[17:42:58] Found seqtk - /usr/local/bin/seqtk
[17:42:58] Found parallel - /usr/local/bin/parallel
[17:42:58] Found freebayes - /usr/local/bin/freebayes
[17:42:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:42:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:42:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:42:58] Found vcfuniq - /usr/local/bin/vcfuniq
[17:42:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:42:58] Found gzip - /bin/gzip
[17:42:58] Found vt - /usr/local/bin/vt
[17:42:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:42:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:42:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:42:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:42:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:42:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:42:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:42:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:44:16] This is snippy 4.6.0Show full stderr[17:44:16] This is snippy 4.6.0
[17:44:16] Written by Torsten Seemann
[17:44:16] Obtained from https://github.com/tseemann/snippy
[17:44:16] Detected operating system: linux
[17:44:16] Enabling bundled linux tools.
[17:44:16] Found bwa - /usr/local/bin/bwa
[17:44:16] Found bcftools - /usr/local/bin/bcftools
[17:44:16] Found samtools - /usr/local/bin/samtools
[17:44:16] Found java - /usr/local/bin/java
[17:44:16] Found snpEff - /usr/local/bin/snpEff
[17:44:16] Found samclip - /usr/local/bin/samclip
[17:44:16] Found seqtk - /usr/local/bin/seqtk
[17:44:16] Found parallel - /usr/local/bin/parallel
[17:44:16] Found freebayes - /usr/local/bin/freebayes
[17:44:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:44:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:44:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:44:16] Found vcfuniq - /usr/local/bin/vcfuniq
[17:44:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:44:16] Found gzip - /bin/gzip
[17:44:16] Found vt - /usr/local/bin/vt
[17:44:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:44:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:44:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:44:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:44:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:44:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:44:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:44:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:45:27] This is snippy 4.6.0Show full stderr[17:45:27] This is snippy 4.6.0
[17:45:27] Written by Torsten Seemann
[17:45:27] Obtained from https://github.com/tseemann/snippy
[17:45:27] Detected operating system: linux
[17:45:27] Enabling bundled linux tools.
[17:45:27] Found bwa - /usr/local/bin/bwa
[17:45:27] Found bcftools - /usr/local/bin/bcftools
[17:45:27] Found samtools - /usr/local/bin/samtools
[17:45:27] Found java - /usr/local/bin/java
[17:45:27] Found snpEff - /usr/local/bin/snpEff
[17:45:27] Found samclip - /usr/local/bin/samclip
[17:45:27] Found seqtk - /usr/local/bin/seqtk
[17:45:27] Found parallel - /usr/local/bin/parallel
[17:45:27] Found freebayes - /usr/local/bin/freebayes
[17:45:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:45:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:45:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:45:27] Found vcfuniq - /usr/local/bin/vcfuniq
[17:45:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:45:27] Found gzip - /bin/gzip
[17:45:27] Found vt - /usr/local/bin/vt
[17:45:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:45:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:45:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:45:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:45:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:45:33] This is snippy 4.6.0Show full stderr[17:45:33] This is snippy 4.6.0
[17:45:33] Written by Torsten Seemann
[17:45:33] Obtained from https://github.com/tseemann/snippy
[17:45:33] Detected operating system: linux
[17:45:33] Enabling bundled linux tools.
[17:45:33] Found bwa - /usr/local/bin/bwa
[17:45:33] Found bcftools - /usr/local/bin/bcftools
[17:45:33] Found samtools - /usr/local/bin/samtools
[17:45:33] Found java - /usr/local/bin/java
[17:45:33] Found snpEff - /usr/local/bin/snpEff
[17:45:33] Found samclip - /usr/local/bin/samclip
[17:45:33] Found seqtk - /usr/local/bin/seqtk
[17:45:33] Found parallel - /usr/local/bin/parallel
[17:45:33] Found freebayes - /usr/local/bin/freebayes
[17:45:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:45:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:45:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:45:33] Found vcfuniq - /usr/local/bin/vcfuniq
[17:45:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:45:33] Found gzip - /bin/gzip
[17:45:33] Found vt - /usr/local/bin/vt
[17:45:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:45:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:45:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:45:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:45:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:45:48] This is snippy 4.6.0Show full stderr[17:45:48] This is snippy 4.6.0
[17:45:48] Written by Torsten Seemann
[17:45:48] Obtained from https://github.com/tseemann/snippy
[17:45:48] Detected operating system: linux
[17:45:48] Enabling bundled linux tools.
[17:45:48] Found bwa - /usr/local/bin/bwa
[17:45:48] Found bcftools - /usr/local/bin/bcftools
[17:45:48] Found samtools - /usr/local/bin/samtools
[17:45:48] Found java - /usr/local/bin/java
[17:45:48] Found snpEff - /usr/local/bin/snpEff
[17:45:48] Found samclip - /usr/local/bin/samclip
[17:45:48] Found seqtk - /usr/local/bin/seqtk
[17:45:48] Found parallel - /usr/local/bin/parallel
[17:45:48] Found freebayes - /usr/local/bin/freebayes
[17:45:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:45:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:45:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:45:48] Found vcfuniq - /usr/local/bin/vcfuniq
[17:45:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:45:48] Found gzip - /bin/gzip
[17:45:48] Found vt - /usr/local/bin/vt
[17:45:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:45:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:45:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:45:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:45:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:45:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:45:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:45:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:46:04] This is snippy 4.6.0Show full stderr[17:46:04] This is snippy 4.6.0
[17:46:04] Written by Torsten Seemann
[17:46:04] Obtained from https://github.com/tseemann/snippy
[17:46:04] Detected operating system: linux
[17:46:04] Enabling bundled linux tools.
[17:46:04] Found bwa - /usr/local/bin/bwa
[17:46:04] Found bcftools - /usr/local/bin/bcftools
[17:46:04] Found samtools - /usr/local/bin/samtools
[17:46:04] Found java - /usr/local/bin/java
[17:46:04] Found snpEff - /usr/local/bin/snpEff
[17:46:04] Found samclip - /usr/local/bin/samclip
[17:46:04] Found seqtk - /usr/local/bin/seqtk
[17:46:04] Found parallel - /usr/local/bin/parallel
[17:46:04] Found freebayes - /usr/local/bin/freebayes
[17:46:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:46:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:46:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:46:05] Found vcfuniq - /usr/local/bin/vcfuniq
[17:46:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:46:05] Found gzip - /bin/gzip
[17:46:05] Found vt - /usr/local/bin/vt
[17:46:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:46:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:46:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:46:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:46:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:46:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:46:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:46:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:46:27] This is snippy 4.6.0Show full stderr[17:46:27] This is snippy 4.6.0
[17:46:27] Written by Torsten Seemann
[17:46:27] Obtained from https://github.com/tseemann/snippy
[17:46:27] Detected operating system: linux
[17:46:27] Enabling bundled linux tools.
[17:46:27] Found bwa - /usr/local/bin/bwa
[17:46:27] Found bcftools - /usr/local/bin/bcftools
[17:46:27] Found samtools - /usr/local/bin/samtools
[17:46:27] Found java - /usr/local/bin/java
[17:46:27] Found snpEff - /usr/local/bin/snpEff
[17:46:27] Found samclip - /usr/local/bin/samclip
[17:46:27] Found seqtk - /usr/local/bin/seqtk
[17:46:27] Found parallel - /usr/local/bin/parallel
[17:46:27] Found freebayes - /usr/local/bin/freebayes
[17:46:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:46:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:46:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:46:27] Found vcfuniq - /usr/local/bin/vcfuniq
[17:46:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:46:27] Found gzip - /bin/gzip
[17:46:27] Found vt - /usr/local/bin/vt
[17:46:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:46:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:46:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:46:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:46:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:46:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:46:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:46:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:52:06] This is snippy 4.6.0Show full stderr[17:52:06] This is snippy 4.6.0
[17:52:06] Written by Torsten Seemann
[17:52:06] Obtained from https://github.com/tseemann/snippy
[17:52:06] Detected operating system: linux
[17:52:06] Enabling bundled linux tools.
[17:52:06] Found bwa - /usr/local/bin/bwa
[17:52:06] Found bcftools - /usr/local/bin/bcftools
[17:52:06] Found samtools - /usr/local/bin/samtools
[17:52:06] Found java - /usr/local/bin/java
[17:52:06] Found snpEff - /usr/local/bin/snpEff
[17:52:06] Found samclip - /usr/local/bin/samclip
[17:52:06] Found seqtk - /usr/local/bin/seqtk
[17:52:06] Found parallel - /usr/local/bin/parallel
[17:52:06] Found freebayes - /usr/local/bin/freebayes
[17:52:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:52:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:52:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:52:07] Found vcfuniq - /usr/local/bin/vcfuniq
[17:52:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:52:07] Found gzip - /bin/gzip
[17:52:07] Found vt - /usr/local/bin/vt
[17:52:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:52:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:52:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:52:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:52:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:52:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:52:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:52:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:48:44] This is snippy 4.6.0Show full stderr[17:48:44] This is snippy 4.6.0
[17:48:44] Written by Torsten Seemann
[17:48:44] Obtained from https://github.com/tseemann/snippy
[17:48:44] Detected operating system: linux
[17:48:44] Enabling bundled linux tools.
[17:48:44] Found bwa - /usr/local/bin/bwa
[17:48:44] Found bcftools - /usr/local/bin/bcftools
[17:48:44] Found samtools - /usr/local/bin/samtools
[17:48:44] Found java - /usr/local/bin/java
[17:48:44] Found snpEff - /usr/local/bin/snpEff
[17:48:44] Found samclip - /usr/local/bin/samclip
[17:48:44] Found seqtk - /usr/local/bin/seqtk
[17:48:44] Found parallel - /usr/local/bin/parallel
[17:48:44] Found freebayes - /usr/local/bin/freebayes
[17:48:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:48:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:48:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:48:44] Found vcfuniq - /usr/local/bin/vcfuniq
[17:48:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:48:44] Found gzip - /bin/gzip
[17:48:44] Found vt - /usr/local/bin/vt
[17:48:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:48:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:48:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:48:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:48:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:48:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:48:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:48:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:52:51] This is snippy 4.6.0Show full stderr[17:52:51] This is snippy 4.6.0
[17:52:51] Written by Torsten Seemann
[17:52:51] Obtained from https://github.com/tseemann/snippy
[17:52:51] Detected operating system: linux
[17:52:51] Enabling bundled linux tools.
[17:52:51] Found bwa - /usr/local/bin/bwa
[17:52:51] Found bcftools - /usr/local/bin/bcftools
[17:52:51] Found samtools - /usr/local/bin/samtools
[17:52:51] Found java - /usr/local/bin/java
[17:52:51] Found snpEff - /usr/local/bin/snpEff
[17:52:51] Found samclip - /usr/local/bin/samclip
[17:52:51] Found seqtk - /usr/local/bin/seqtk
[17:52:51] Found parallel - /usr/local/bin/parallel
[17:52:51] Found freebayes - /usr/local/bin/freebayes
[17:52:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:52:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:52:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:52:51] Found vcfuniq - /usr/local/bin/vcfuniq
[17:52:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:52:51] Found gzip - /bin/gzip
[17:52:51] Found vt - /usr/local/bin/vt
[17:52:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:52:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:52:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:52:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:52:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:52:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:52:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:52:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:56:28] This is snippy 4.6.0Show full stderr[17:56:28] This is snippy 4.6.0
[17:56:28] Written by Torsten Seemann
[17:56:28] Obtained from https://github.com/tseemann/snippy
[17:56:28] Detected operating system: linux
[17:56:28] Enabling bundled linux tools.
[17:56:28] Found bwa - /usr/local/bin/bwa
[17:56:28] Found bcftools - /usr/local/bin/bcftools
[17:56:28] Found samtools - /usr/local/bin/samtools
[17:56:28] Found java - /usr/local/bin/java
[17:56:28] Found snpEff - /usr/local/bin/snpEff
[17:56:28] Found samclip - /usr/local/bin/samclip
[17:56:28] Found seqtk - /usr/local/bin/seqtk
[17:56:28] Found parallel - /usr/local/bin/parallel
[17:56:28] Found freebayes - /usr/local/bin/freebayes
[17:56:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:56:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:56:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:56:28] Found vcfuniq - /usr/local/bin/vcfuniq
[17:56:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:56:28] Found gzip - /bin/gzip
[17:56:28] Found vt - /usr/local/bin/vt
[17:56:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:56:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:56:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:56:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:56:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:56:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:56:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:56:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:51:28] This is snippy 4.6.0Show full stderr[17:51:28] This is snippy 4.6.0
[17:51:28] Written by Torsten Seemann
[17:51:28] Obtained from https://github.com/tseemann/snippy
[17:51:28] Detected operating system: linux
[17:51:28] Enabling bundled linux tools.
[17:51:28] Found bwa - /usr/local/bin/bwa
[17:51:28] Found bcftools - /usr/local/bin/bcftools
[17:51:28] Found samtools - /usr/local/bin/samtools
[17:51:28] Found java - /usr/local/bin/java
[17:51:29] Found snpEff - /usr/local/bin/snpEff
[17:51:29] Found samclip - /usr/local/bin/samclip
[17:51:29] Found seqtk - /usr/local/bin/seqtk
[17:51:29] Found parallel - /usr/local/bin/parallel
[17:51:29] Found freebayes - /usr/local/bin/freebayes
[17:51:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:51:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:51:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:51:29] Found vcfuniq - /usr/local/bin/vcfuniq
[17:51:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:51:29] Found gzip - /bin/gzip
[17:51:29] Found vt - /usr/local/bin/vt
[17:51:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:51:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:51:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:51:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:51:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:51:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:51:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:51:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:51:55] This is snippy 4.6.0Show full stderr[17:51:55] This is snippy 4.6.0
[17:51:55] Written by Torsten Seemann
[17:51:55] Obtained from https://github.com/tseemann/snippy
[17:51:55] Detected operating system: linux
[17:51:55] Enabling bundled linux tools.
[17:51:55] Found bwa - /usr/local/bin/bwa
[17:51:55] Found bcftools - /usr/local/bin/bcftools
[17:51:55] Found samtools - /usr/local/bin/samtools
[17:51:55] Found java - /usr/local/bin/java
[17:51:55] Found snpEff - /usr/local/bin/snpEff
[17:51:55] Found samclip - /usr/local/bin/samclip
[17:51:55] Found seqtk - /usr/local/bin/seqtk
[17:51:55] Found parallel - /usr/local/bin/parallel
[17:51:55] Found freebayes - /usr/local/bin/freebayes
[17:51:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:51:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:51:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:51:55] Found vcfuniq - /usr/local/bin/vcfuniq
[17:51:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:51:55] Found gzip - /bin/gzip
[17:51:55] Found vt - /usr/local/bin/vt
[17:51:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:51:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:51:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:51:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:51:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:51:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:51:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:51:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:56:37] This is snippy 4.6.0Show full stderr[17:56:37] This is snippy 4.6.0
[17:56:37] Written by Torsten Seemann
[17:56:37] Obtained from https://github.com/tseemann/snippy
[17:56:37] Detected operating system: linux
[17:56:37] Enabling bundled linux tools.
[17:56:37] Found bwa - /usr/local/bin/bwa
[17:56:37] Found bcftools - /usr/local/bin/bcftools
[17:56:37] Found samtools - /usr/local/bin/samtools
[17:56:37] Found java - /usr/local/bin/java
[17:56:37] Found snpEff - /usr/local/bin/snpEff
[17:56:37] Found samclip - /usr/local/bin/samclip
[17:56:37] Found seqtk - /usr/local/bin/seqtk
[17:56:37] Found parallel - /usr/local/bin/parallel
[17:56:37] Found freebayes - /usr/local/bin/freebayes
[17:56:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:56:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:56:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:56:37] Found vcfuniq - /usr/local/bin/vcfuniq
[17:56:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:56:37] Found gzip - /bin/gzip
[17:56:37] Found vt - /usr/local/bin/vt
[17:56:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:56:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:56:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:56:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:56:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:56:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:56:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:56:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [17:52:37] This is snippy 4.6.0Show full stderr[17:52:37] This is snippy 4.6.0
[17:52:37] Written by Torsten Seemann
[17:52:37] Obtained from https://github.com/tseemann/snippy
[17:52:37] Detected operating system: linux
[17:52:37] Enabling bundled linux tools.
[17:52:37] Found bwa - /usr/local/bin/bwa
[17:52:37] Found bcftools - /usr/local/bin/bcftools
[17:52:37] Found samtools - /usr/local/bin/samtools
[17:52:37] Found java - /usr/local/bin/java
[17:52:37] Found snpEff - /usr/local/bin/snpEff
[17:52:37] Found samclip - /usr/local/bin/samclip
[17:52:37] Found seqtk - /usr/local/bin/seqtk
[17:52:37] Found parallel - /usr/local/bin/parallel
[17:52:37] Found freebayes - /usr/local/bin/freebayes
[17:52:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:52:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:52:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:52:37] Found vcfuniq - /usr/local/bin/vcfuniq
[17:52:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:52:37] Found gzip - /bin/gzip
[17:52:37] Found vt - /usr/local/bin/vt
[17:52:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:52:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:52:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:52:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:52:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:52:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:52:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:52:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:22:44] This is snippy 4.6.0Show full stderr[00:22:44] This is snippy 4.6.0
[00:22:44] Written by Torsten Seemann
[00:22:44] Obtained from https://github.com/tseemann/snippy
[00:22:44] Detected operating system: linux
[00:22:44] Enabling bundled linux tools.
[00:22:44] Found bwa - /usr/local/bin/bwa
[00:22:44] Found bcftools - /usr/local/bin/bcftools
[00:22:44] Found samtools - /usr/local/bin/samtools
[00:22:44] Found java - /usr/local/bin/java
[00:22:44] Found snpEff - /usr/local/bin/snpEff
[00:22:44] Found samclip - /usr/local/bin/samclip
[00:22:44] Found seqtk - /usr/local/bin/seqtk
[00:22:44] Found parallel - /usr/local/bin/parallel
[00:22:44] Found freebayes - /usr/local/bin/freebayes
[00:22:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:22:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:22:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:22:44] Found vcfuniq - /usr/local/bin/vcfuniq
[00:22:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:22:44] Found gzip - /bin/gzip
[00:22:44] Found vt - /usr/local/bin/vt
[00:22:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:22:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:22:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:22:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:22:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:22:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:22:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:22:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:23:07] This is snippy 4.6.0Show full stderr[00:23:07] This is snippy 4.6.0
[00:23:07] Written by Torsten Seemann
[00:23:07] Obtained from https://github.com/tseemann/snippy
[00:23:07] Detected operating system: linux
[00:23:07] Enabling bundled linux tools.
[00:23:07] Found bwa - /usr/local/bin/bwa
[00:23:07] Found bcftools - /usr/local/bin/bcftools
[00:23:07] Found samtools - /usr/local/bin/samtools
[00:23:07] Found java - /usr/local/bin/java
[00:23:07] Found snpEff - /usr/local/bin/snpEff
[00:23:07] Found samclip - /usr/local/bin/samclip
[00:23:07] Found seqtk - /usr/local/bin/seqtk
[00:23:07] Found parallel - /usr/local/bin/parallel
[00:23:07] Found freebayes - /usr/local/bin/freebayes
[00:23:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:07] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:07] Found gzip - /bin/gzip
[00:23:07] Found vt - /usr/local/bin/vt
[00:23:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:23:14] This is snippy 4.6.0Show full stderr[00:23:14] This is snippy 4.6.0
[00:23:14] Written by Torsten Seemann
[00:23:14] Obtained from https://github.com/tseemann/snippy
[00:23:14] Detected operating system: linux
[00:23:14] Enabling bundled linux tools.
[00:23:14] Found bwa - /usr/local/bin/bwa
[00:23:14] Found bcftools - /usr/local/bin/bcftools
[00:23:14] Found samtools - /usr/local/bin/samtools
[00:23:14] Found java - /usr/local/bin/java
[00:23:14] Found snpEff - /usr/local/bin/snpEff
[00:23:14] Found samclip - /usr/local/bin/samclip
[00:23:14] Found seqtk - /usr/local/bin/seqtk
[00:23:14] Found parallel - /usr/local/bin/parallel
[00:23:14] Found freebayes - /usr/local/bin/freebayes
[00:23:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:15] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:15] Found gzip - /bin/gzip
[00:23:15] Found vt - /usr/local/bin/vt
[00:23:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:23:32] This is snippy 4.6.0Show full stderr[00:23:32] This is snippy 4.6.0
[00:23:32] Written by Torsten Seemann
[00:23:32] Obtained from https://github.com/tseemann/snippy
[00:23:32] Detected operating system: linux
[00:23:32] Enabling bundled linux tools.
[00:23:32] Found bwa - /usr/local/bin/bwa
[00:23:32] Found bcftools - /usr/local/bin/bcftools
[00:23:32] Found samtools - /usr/local/bin/samtools
[00:23:32] Found java - /usr/local/bin/java
[00:23:32] Found snpEff - /usr/local/bin/snpEff
[00:23:32] Found samclip - /usr/local/bin/samclip
[00:23:32] Found seqtk - /usr/local/bin/seqtk
[00:23:32] Found parallel - /usr/local/bin/parallel
[00:23:32] Found freebayes - /usr/local/bin/freebayes
[00:23:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:32] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:32] Found gzip - /bin/gzip
[00:23:32] Found vt - /usr/local/bin/vt
[00:23:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:23:54] This is snippy 4.6.0Show full stderr[00:23:54] This is snippy 4.6.0
[00:23:54] Written by Torsten Seemann
[00:23:54] Obtained from https://github.com/tseemann/snippy
[00:23:54] Detected operating system: linux
[00:23:54] Enabling bundled linux tools.
[00:23:54] Found bwa - /usr/local/bin/bwa
[00:23:54] Found bcftools - /usr/local/bin/bcftools
[00:23:54] Found samtools - /usr/local/bin/samtools
[00:23:54] Found java - /usr/local/bin/java
[00:23:54] Found snpEff - /usr/local/bin/snpEff
[00:23:54] Found samclip - /usr/local/bin/samclip
[00:23:54] Found seqtk - /usr/local/bin/seqtk
[00:23:54] Found parallel - /usr/local/bin/parallel
[00:23:54] Found freebayes - /usr/local/bin/freebayes
[00:23:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:54] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:54] Found gzip - /bin/gzip
[00:23:54] Found vt - /usr/local/bin/vt
[00:23:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:25:24] This is snippy 4.6.0Show full stderr[00:25:24] This is snippy 4.6.0
[00:25:24] Written by Torsten Seemann
[00:25:24] Obtained from https://github.com/tseemann/snippy
[00:25:24] Detected operating system: linux
[00:25:24] Enabling bundled linux tools.
[00:25:24] Found bwa - /usr/local/bin/bwa
[00:25:24] Found bcftools - /usr/local/bin/bcftools
[00:25:24] Found samtools - /usr/local/bin/samtools
[00:25:24] Found java - /usr/local/bin/java
[00:25:24] Found snpEff - /usr/local/bin/snpEff
[00:25:24] Found samclip - /usr/local/bin/samclip
[00:25:24] Found seqtk - /usr/local/bin/seqtk
[00:25:24] Found parallel - /usr/local/bin/parallel
[00:25:24] Found freebayes - /usr/local/bin/freebayes
[00:25:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:25:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:25:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:25:24] Found vcfuniq - /usr/local/bin/vcfuniq
[00:25:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:25:24] Found gzip - /bin/gzip
[00:25:24] Found vt - /usr/local/bin/vt
[00:25:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:25:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:25:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:25:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:25:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:25:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:25:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:25:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:24:30] This is snippy 4.6.0Show full stderr[00:24:30] This is snippy 4.6.0
[00:24:30] Written by Torsten Seemann
[00:24:30] Obtained from https://github.com/tseemann/snippy
[00:24:30] Detected operating system: linux
[00:24:30] Enabling bundled linux tools.
[00:24:30] Found bwa - /usr/local/bin/bwa
[00:24:30] Found bcftools - /usr/local/bin/bcftools
[00:24:30] Found samtools - /usr/local/bin/samtools
[00:24:30] Found java - /usr/local/bin/java
[00:24:30] Found snpEff - /usr/local/bin/snpEff
[00:24:30] Found samclip - /usr/local/bin/samclip
[00:24:30] Found seqtk - /usr/local/bin/seqtk
[00:24:30] Found parallel - /usr/local/bin/parallel
[00:24:30] Found freebayes - /usr/local/bin/freebayes
[00:24:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:24:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:24:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:24:31] Found vcfuniq - /usr/local/bin/vcfuniq
[00:24:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:24:31] Found gzip - /bin/gzip
[00:24:31] Found vt - /usr/local/bin/vt
[00:24:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:24:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:24:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:24:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:24:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:24:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:24:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:24:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:23:29] This is snippy 4.6.0Show full stderr[00:23:29] This is snippy 4.6.0
[00:23:29] Written by Torsten Seemann
[00:23:29] Obtained from https://github.com/tseemann/snippy
[00:23:29] Detected operating system: linux
[00:23:29] Enabling bundled linux tools.
[00:23:29] Found bwa - /usr/local/bin/bwa
[00:23:29] Found bcftools - /usr/local/bin/bcftools
[00:23:29] Found samtools - /usr/local/bin/samtools
[00:23:29] Found java - /usr/local/bin/java
[00:23:29] Found snpEff - /usr/local/bin/snpEff
[00:23:29] Found samclip - /usr/local/bin/samclip
[00:23:29] Found seqtk - /usr/local/bin/seqtk
[00:23:29] Found parallel - /usr/local/bin/parallel
[00:23:29] Found freebayes - /usr/local/bin/freebayes
[00:23:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:29] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:29] Found gzip - /bin/gzip
[00:23:29] Found vt - /usr/local/bin/vt
[00:23:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:24:09] This is snippy 4.6.0Show full stderr[00:24:09] This is snippy 4.6.0
[00:24:09] Written by Torsten Seemann
[00:24:09] Obtained from https://github.com/tseemann/snippy
[00:24:09] Detected operating system: linux
[00:24:09] Enabling bundled linux tools.
[00:24:09] Found bwa - /usr/local/bin/bwa
[00:24:09] Found bcftools - /usr/local/bin/bcftools
[00:24:09] Found samtools - /usr/local/bin/samtools
[00:24:09] Found java - /usr/local/bin/java
[00:24:09] Found snpEff - /usr/local/bin/snpEff
[00:24:09] Found samclip - /usr/local/bin/samclip
[00:24:09] Found seqtk - /usr/local/bin/seqtk
[00:24:09] Found parallel - /usr/local/bin/parallel
[00:24:09] Found freebayes - /usr/local/bin/freebayes
[00:24:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:24:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:24:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:24:09] Found vcfuniq - /usr/local/bin/vcfuniq
[00:24:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:24:09] Found gzip - /bin/gzip
[00:24:09] Found vt - /usr/local/bin/vt
[00:24:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:24:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:24:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:24:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:24:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:24:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:24:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:24:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:25:23] This is snippy 4.6.0Show full stderr[00:25:23] This is snippy 4.6.0
[00:25:23] Written by Torsten Seemann
[00:25:23] Obtained from https://github.com/tseemann/snippy
[00:25:23] Detected operating system: linux
[00:25:23] Enabling bundled linux tools.
[00:25:23] Found bwa - /usr/local/bin/bwa
[00:25:23] Found bcftools - /usr/local/bin/bcftools
[00:25:23] Found samtools - /usr/local/bin/samtools
[00:25:23] Found java - /usr/local/bin/java
[00:25:23] Found snpEff - /usr/local/bin/snpEff
[00:25:23] Found samclip - /usr/local/bin/samclip
[00:25:23] Found seqtk - /usr/local/bin/seqtk
[00:25:23] Found parallel - /usr/local/bin/parallel
[00:25:23] Found freebayes - /usr/local/bin/freebayes
[00:25:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:25:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:25:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:25:23] Found vcfuniq - /usr/local/bin/vcfuniq
[00:25:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:25:23] Found gzip - /bin/gzip
[00:25:23] Found vt - /usr/local/bin/vt
[00:25:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:25:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:25:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:25:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:25:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:25:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:25:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:25:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:25:30] This is snippy 4.6.0Show full stderr[00:25:30] This is snippy 4.6.0
[00:25:30] Written by Torsten Seemann
[00:25:30] Obtained from https://github.com/tseemann/snippy
[00:25:30] Detected operating system: linux
[00:25:30] Enabling bundled linux tools.
[00:25:30] Found bwa - /usr/local/bin/bwa
[00:25:30] Found bcftools - /usr/local/bin/bcftools
[00:25:30] Found samtools - /usr/local/bin/samtools
[00:25:30] Found java - /usr/local/bin/java
[00:25:30] Found snpEff - /usr/local/bin/snpEff
[00:25:30] Found samclip - /usr/local/bin/samclip
[00:25:30] Found seqtk - /usr/local/bin/seqtk
[00:25:30] Found parallel - /usr/local/bin/parallel
[00:25:30] Found freebayes - /usr/local/bin/freebayes
[00:25:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:25:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:25:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:25:30] Found vcfuniq - /usr/local/bin/vcfuniq
[00:25:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:25:30] Found gzip - /bin/gzip
[00:25:30] Found vt - /usr/local/bin/vt
[00:25:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:25:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:25:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:25:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:25:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:25:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:25:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:25:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:26:09] This is snippy 4.6.0Show full stderr[00:26:09] This is snippy 4.6.0
[00:26:09] Written by Torsten Seemann
[00:26:09] Obtained from https://github.com/tseemann/snippy
[00:26:09] Detected operating system: linux
[00:26:09] Enabling bundled linux tools.
[00:26:09] Found bwa - /usr/local/bin/bwa
[00:26:09] Found bcftools - /usr/local/bin/bcftools
[00:26:09] Found samtools - /usr/local/bin/samtools
[00:26:09] Found java - /usr/local/bin/java
[00:26:10] Found snpEff - /usr/local/bin/snpEff
[00:26:10] Found samclip - /usr/local/bin/samclip
[00:26:10] Found seqtk - /usr/local/bin/seqtk
[00:26:10] Found parallel - /usr/local/bin/parallel
[00:26:10] Found freebayes - /usr/local/bin/freebayes
[00:26:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:10] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:10] Found gzip - /bin/gzip
[00:26:10] Found vt - /usr/local/bin/vt
[00:26:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:26:22] This is snippy 4.6.0Show full stderr[00:26:22] This is snippy 4.6.0
[00:26:22] Written by Torsten Seemann
[00:26:22] Obtained from https://github.com/tseemann/snippy
[00:26:22] Detected operating system: linux
[00:26:22] Enabling bundled linux tools.
[00:26:22] Found bwa - /usr/local/bin/bwa
[00:26:22] Found bcftools - /usr/local/bin/bcftools
[00:26:22] Found samtools - /usr/local/bin/samtools
[00:26:22] Found java - /usr/local/bin/java
[00:26:22] Found snpEff - /usr/local/bin/snpEff
[00:26:22] Found samclip - /usr/local/bin/samclip
[00:26:22] Found seqtk - /usr/local/bin/seqtk
[00:26:22] Found parallel - /usr/local/bin/parallel
[00:26:22] Found freebayes - /usr/local/bin/freebayes
[00:26:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:22] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:22] Found gzip - /bin/gzip
[00:26:22] Found vt - /usr/local/bin/vt
[00:26:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:26:27] This is snippy 4.6.0Show full stderr[00:26:27] This is snippy 4.6.0
[00:26:27] Written by Torsten Seemann
[00:26:27] Obtained from https://github.com/tseemann/snippy
[00:26:27] Detected operating system: linux
[00:26:27] Enabling bundled linux tools.
[00:26:27] Found bwa - /usr/local/bin/bwa
[00:26:27] Found bcftools - /usr/local/bin/bcftools
[00:26:27] Found samtools - /usr/local/bin/samtools
[00:26:27] Found java - /usr/local/bin/java
[00:26:27] Found snpEff - /usr/local/bin/snpEff
[00:26:27] Found samclip - /usr/local/bin/samclip
[00:26:27] Found seqtk - /usr/local/bin/seqtk
[00:26:27] Found parallel - /usr/local/bin/parallel
[00:26:27] Found freebayes - /usr/local/bin/freebayes
[00:26:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:27] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:27] Found gzip - /bin/gzip
[00:26:27] Found vt - /usr/local/bin/vt
[00:26:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:26:33] This is snippy 4.6.0Show full stderr[00:26:33] This is snippy 4.6.0
[00:26:33] Written by Torsten Seemann
[00:26:33] Obtained from https://github.com/tseemann/snippy
[00:26:33] Detected operating system: linux
[00:26:33] Enabling bundled linux tools.
[00:26:33] Found bwa - /usr/local/bin/bwa
[00:26:33] Found bcftools - /usr/local/bin/bcftools
[00:26:33] Found samtools - /usr/local/bin/samtools
[00:26:33] Found java - /usr/local/bin/java
[00:26:33] Found snpEff - /usr/local/bin/snpEff
[00:26:33] Found samclip - /usr/local/bin/samclip
[00:26:33] Found seqtk - /usr/local/bin/seqtk
[00:26:33] Found parallel - /usr/local/bin/parallel
[00:26:33] Found freebayes - /usr/local/bin/freebayes
[00:26:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:33] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:33] Found gzip - /bin/gzip
[00:26:33] Found vt - /usr/local/bin/vt
[00:26:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:27:00] This is snippy 4.6.0Show full stderr[00:27:00] This is snippy 4.6.0
[00:27:00] Written by Torsten Seemann
[00:27:00] Obtained from https://github.com/tseemann/snippy
[00:27:00] Detected operating system: linux
[00:27:00] Enabling bundled linux tools.
[00:27:00] Found bwa - /usr/local/bin/bwa
[00:27:00] Found bcftools - /usr/local/bin/bcftools
[00:27:00] Found samtools - /usr/local/bin/samtools
[00:27:00] Found java - /usr/local/bin/java
[00:27:00] Found snpEff - /usr/local/bin/snpEff
[00:27:00] Found samclip - /usr/local/bin/samclip
[00:27:00] Found seqtk - /usr/local/bin/seqtk
[00:27:00] Found parallel - /usr/local/bin/parallel
[00:27:00] Found freebayes - /usr/local/bin/freebayes
[00:27:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:27:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:27:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:27:00] Found vcfuniq - /usr/local/bin/vcfuniq
[00:27:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:27:00] Found gzip - /bin/gzip
[00:27:00] Found vt - /usr/local/bin/vt
[00:27:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:27:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:27:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:27:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:27:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:27:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:27:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:27:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:23:16] This is snippy 4.6.0Show full stderr[00:23:16] This is snippy 4.6.0
[00:23:16] Written by Torsten Seemann
[00:23:16] Obtained from https://github.com/tseemann/snippy
[00:23:16] Detected operating system: linux
[00:23:16] Enabling bundled linux tools.
[00:23:16] Found bwa - /usr/local/bin/bwa
[00:23:16] Found bcftools - /usr/local/bin/bcftools
[00:23:17] Found samtools - /usr/local/bin/samtools
[00:23:17] Found java - /usr/local/bin/java
[00:23:17] Found snpEff - /usr/local/bin/snpEff
[00:23:17] Found samclip - /usr/local/bin/samclip
[00:23:17] Found seqtk - /usr/local/bin/seqtk
[00:23:17] Found parallel - /usr/local/bin/parallel
[00:23:17] Found freebayes - /usr/local/bin/freebayes
[00:23:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:17] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:17] Found gzip - /bin/gzip
[00:23:17] Found vt - /usr/local/bin/vt
[00:23:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:23:13] This is snippy 4.6.0Show full stderr[00:23:13] This is snippy 4.6.0
[00:23:13] Written by Torsten Seemann
[00:23:13] Obtained from https://github.com/tseemann/snippy
[00:23:13] Detected operating system: linux
[00:23:13] Enabling bundled linux tools.
[00:23:13] Found bwa - /usr/local/bin/bwa
[00:23:13] Found bcftools - /usr/local/bin/bcftools
[00:23:13] Found samtools - /usr/local/bin/samtools
[00:23:13] Found java - /usr/local/bin/java
[00:23:13] Found snpEff - /usr/local/bin/snpEff
[00:23:13] Found samclip - /usr/local/bin/samclip
[00:23:13] Found seqtk - /usr/local/bin/seqtk
[00:23:13] Found parallel - /usr/local/bin/parallel
[00:23:13] Found freebayes - /usr/local/bin/freebayes
[00:23:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:13] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:13] Found gzip - /bin/gzip
[00:23:13] Found vt - /usr/local/bin/vt
[00:23:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:02] This is snippy 4.6.0Show full stderr[00:29:02] This is snippy 4.6.0
[00:29:02] Written by Torsten Seemann
[00:29:02] Obtained from https://github.com/tseemann/snippy
[00:29:02] Detected operating system: linux
[00:29:02] Enabling bundled linux tools.
[00:29:03] Found bwa - /usr/local/bin/bwa
[00:29:03] Found bcftools - /usr/local/bin/bcftools
[00:29:03] Found samtools - /usr/local/bin/samtools
[00:29:03] Found java - /usr/local/bin/java
[00:29:03] Found snpEff - /usr/local/bin/snpEff
[00:29:03] Found samclip - /usr/local/bin/samclip
[00:29:03] Found seqtk - /usr/local/bin/seqtk
[00:29:03] Found parallel - /usr/local/bin/parallel
[00:29:03] Found freebayes - /usr/local/bin/freebayes
[00:29:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:03] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:03] Found gzip - /bin/gzip
[00:29:03] Found vt - /usr/local/bin/vt
[00:29:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:36] This is snippy 4.6.0Show full stderr[00:29:36] This is snippy 4.6.0
[00:29:36] Written by Torsten Seemann
[00:29:36] Obtained from https://github.com/tseemann/snippy
[00:29:36] Detected operating system: linux
[00:29:36] Enabling bundled linux tools.
[00:29:36] Found bwa - /usr/local/bin/bwa
[00:29:36] Found bcftools - /usr/local/bin/bcftools
[00:29:36] Found samtools - /usr/local/bin/samtools
[00:29:36] Found java - /usr/local/bin/java
[00:29:36] Found snpEff - /usr/local/bin/snpEff
[00:29:36] Found samclip - /usr/local/bin/samclip
[00:29:36] Found seqtk - /usr/local/bin/seqtk
[00:29:36] Found parallel - /usr/local/bin/parallel
[00:29:36] Found freebayes - /usr/local/bin/freebayes
[00:29:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:36] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:36] Found gzip - /bin/gzip
[00:29:36] Found vt - /usr/local/bin/vt
[00:29:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:41] This is snippy 4.6.0Show full stderr[00:29:41] This is snippy 4.6.0
[00:29:41] Written by Torsten Seemann
[00:29:41] Obtained from https://github.com/tseemann/snippy
[00:29:41] Detected operating system: linux
[00:29:41] Enabling bundled linux tools.
[00:29:42] Found bwa - /usr/local/bin/bwa
[00:29:42] Found bcftools - /usr/local/bin/bcftools
[00:29:42] Found samtools - /usr/local/bin/samtools
[00:29:42] Found java - /usr/local/bin/java
[00:29:42] Found snpEff - /usr/local/bin/snpEff
[00:29:42] Found samclip - /usr/local/bin/samclip
[00:29:42] Found seqtk - /usr/local/bin/seqtk
[00:29:42] Found parallel - /usr/local/bin/parallel
[00:29:42] Found freebayes - /usr/local/bin/freebayes
[00:29:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:42] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:42] Found gzip - /bin/gzip
[00:29:42] Found vt - /usr/local/bin/vt
[00:29:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:24:50] This is snippy 4.6.0Show full stderr[00:24:50] This is snippy 4.6.0
[00:24:50] Written by Torsten Seemann
[00:24:50] Obtained from https://github.com/tseemann/snippy
[00:24:50] Detected operating system: linux
[00:24:50] Enabling bundled linux tools.
[00:24:50] Found bwa - /usr/local/bin/bwa
[00:24:50] Found bcftools - /usr/local/bin/bcftools
[00:24:50] Found samtools - /usr/local/bin/samtools
[00:24:50] Found java - /usr/local/bin/java
[00:24:50] Found snpEff - /usr/local/bin/snpEff
[00:24:50] Found samclip - /usr/local/bin/samclip
[00:24:50] Found seqtk - /usr/local/bin/seqtk
[00:24:50] Found parallel - /usr/local/bin/parallel
[00:24:50] Found freebayes - /usr/local/bin/freebayes
[00:24:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:24:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:24:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:24:50] Found vcfuniq - /usr/local/bin/vcfuniq
[00:24:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:24:50] Found gzip - /bin/gzip
[00:24:50] Found vt - /usr/local/bin/vt
[00:24:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:24:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:24:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:24:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:24:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:24:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:24:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:24:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:26:39] This is snippy 4.6.0Show full stderr[00:26:39] This is snippy 4.6.0
[00:26:39] Written by Torsten Seemann
[00:26:39] Obtained from https://github.com/tseemann/snippy
[00:26:39] Detected operating system: linux
[00:26:39] Enabling bundled linux tools.
[00:26:39] Found bwa - /usr/local/bin/bwa
[00:26:39] Found bcftools - /usr/local/bin/bcftools
[00:26:39] Found samtools - /usr/local/bin/samtools
[00:26:39] Found java - /usr/local/bin/java
[00:26:39] Found snpEff - /usr/local/bin/snpEff
[00:26:39] Found samclip - /usr/local/bin/samclip
[00:26:39] Found seqtk - /usr/local/bin/seqtk
[00:26:39] Found parallel - /usr/local/bin/parallel
[00:26:39] Found freebayes - /usr/local/bin/freebayes
[00:26:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:39] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:39] Found gzip - /bin/gzip
[00:26:39] Found vt - /usr/local/bin/vt
[00:26:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:25:54] This is snippy 4.6.0Show full stderr[00:25:54] This is snippy 4.6.0
[00:25:54] Written by Torsten Seemann
[00:25:54] Obtained from https://github.com/tseemann/snippy
[00:25:54] Detected operating system: linux
[00:25:54] Enabling bundled linux tools.
[00:25:54] Found bwa - /usr/local/bin/bwa
[00:25:54] Found bcftools - /usr/local/bin/bcftools
[00:25:54] Found samtools - /usr/local/bin/samtools
[00:25:54] Found java - /usr/local/bin/java
[00:25:54] Found snpEff - /usr/local/bin/snpEff
[00:25:54] Found samclip - /usr/local/bin/samclip
[00:25:54] Found seqtk - /usr/local/bin/seqtk
[00:25:54] Found parallel - /usr/local/bin/parallel
[00:25:54] Found freebayes - /usr/local/bin/freebayes
[00:25:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:25:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:25:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:25:54] Found vcfuniq - /usr/local/bin/vcfuniq
[00:25:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:25:54] Found gzip - /bin/gzip
[00:25:54] Found vt - /usr/local/bin/vt
[00:25:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:25:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:25:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:25:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:25:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:25:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:25:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:25:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:26:01] This is snippy 4.6.0Show full stderr[00:26:01] This is snippy 4.6.0
[00:26:01] Written by Torsten Seemann
[00:26:01] Obtained from https://github.com/tseemann/snippy
[00:26:01] Detected operating system: linux
[00:26:01] Enabling bundled linux tools.
[00:26:01] Found bwa - /usr/local/bin/bwa
[00:26:01] Found bcftools - /usr/local/bin/bcftools
[00:26:01] Found samtools - /usr/local/bin/samtools
[00:26:01] Found java - /usr/local/bin/java
[00:26:01] Found snpEff - /usr/local/bin/snpEff
[00:26:01] Found samclip - /usr/local/bin/samclip
[00:26:01] Found seqtk - /usr/local/bin/seqtk
[00:26:01] Found parallel - /usr/local/bin/parallel
[00:26:01] Found freebayes - /usr/local/bin/freebayes
[00:26:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:01] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:01] Found gzip - /bin/gzip
[00:26:01] Found vt - /usr/local/bin/vt
[00:26:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:27:06] This is snippy 4.6.0Show full stderr[00:27:06] This is snippy 4.6.0
[00:27:06] Written by Torsten Seemann
[00:27:06] Obtained from https://github.com/tseemann/snippy
[00:27:06] Detected operating system: linux
[00:27:06] Enabling bundled linux tools.
[00:27:06] Found bwa - /usr/local/bin/bwa
[00:27:06] Found bcftools - /usr/local/bin/bcftools
[00:27:06] Found samtools - /usr/local/bin/samtools
[00:27:06] Found java - /usr/local/bin/java
[00:27:06] Found snpEff - /usr/local/bin/snpEff
[00:27:06] Found samclip - /usr/local/bin/samclip
[00:27:06] Found seqtk - /usr/local/bin/seqtk
[00:27:06] Found parallel - /usr/local/bin/parallel
[00:27:06] Found freebayes - /usr/local/bin/freebayes
[00:27:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:27:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:27:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:27:06] Found vcfuniq - /usr/local/bin/vcfuniq
[00:27:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:27:06] Found gzip - /bin/gzip
[00:27:06] Found vt - /usr/local/bin/vt
[00:27:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:27:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:27:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:27:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:27:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:27:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:27:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:27:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:44] This is snippy 4.6.0Show full stderr[00:29:44] This is snippy 4.6.0
[00:29:44] Written by Torsten Seemann
[00:29:44] Obtained from https://github.com/tseemann/snippy
[00:29:44] Detected operating system: linux
[00:29:44] Enabling bundled linux tools.
[00:29:44] Found bwa - /usr/local/bin/bwa
[00:29:44] Found bcftools - /usr/local/bin/bcftools
[00:29:44] Found samtools - /usr/local/bin/samtools
[00:29:44] Found java - /usr/local/bin/java
[00:29:44] Found snpEff - /usr/local/bin/snpEff
[00:29:44] Found samclip - /usr/local/bin/samclip
[00:29:44] Found seqtk - /usr/local/bin/seqtk
[00:29:44] Found parallel - /usr/local/bin/parallel
[00:29:44] Found freebayes - /usr/local/bin/freebayes
[00:29:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:44] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:44] Found gzip - /bin/gzip
[00:29:44] Found vt - /usr/local/bin/vt
[00:29:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:28:53] This is snippy 4.6.0Show full stderr[00:28:53] This is snippy 4.6.0
[00:28:53] Written by Torsten Seemann
[00:28:53] Obtained from https://github.com/tseemann/snippy
[00:28:53] Detected operating system: linux
[00:28:53] Enabling bundled linux tools.
[00:28:53] Found bwa - /usr/local/bin/bwa
[00:28:53] Found bcftools - /usr/local/bin/bcftools
[00:28:53] Found samtools - /usr/local/bin/samtools
[00:28:53] Found java - /usr/local/bin/java
[00:28:54] Found snpEff - /usr/local/bin/snpEff
[00:28:54] Found samclip - /usr/local/bin/samclip
[00:28:54] Found seqtk - /usr/local/bin/seqtk
[00:28:54] Found parallel - /usr/local/bin/parallel
[00:28:54] Found freebayes - /usr/local/bin/freebayes
[00:28:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:28:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:28:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:28:54] Found vcfuniq - /usr/local/bin/vcfuniq
[00:28:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:28:54] Found gzip - /bin/gzip
[00:28:54] Found vt - /usr/local/bin/vt
[00:28:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:28:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:28:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:28:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:28:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:28:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:28:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:28:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:05] This is snippy 4.6.0Show full stderr[00:29:05] This is snippy 4.6.0
[00:29:05] Written by Torsten Seemann
[00:29:05] Obtained from https://github.com/tseemann/snippy
[00:29:05] Detected operating system: linux
[00:29:05] Enabling bundled linux tools.
[00:29:05] Found bwa - /usr/local/bin/bwa
[00:29:05] Found bcftools - /usr/local/bin/bcftools
[00:29:05] Found samtools - /usr/local/bin/samtools
[00:29:05] Found java - /usr/local/bin/java
[00:29:05] Found snpEff - /usr/local/bin/snpEff
[00:29:05] Found samclip - /usr/local/bin/samclip
[00:29:06] Found seqtk - /usr/local/bin/seqtk
[00:29:06] Found parallel - /usr/local/bin/parallel
[00:29:06] Found freebayes - /usr/local/bin/freebayes
[00:29:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:06] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:06] Found gzip - /bin/gzip
[00:29:06] Found vt - /usr/local/bin/vt
[00:29:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:12] This is snippy 4.6.0Show full stderr[00:29:12] This is snippy 4.6.0
[00:29:12] Written by Torsten Seemann
[00:29:12] Obtained from https://github.com/tseemann/snippy
[00:29:12] Detected operating system: linux
[00:29:12] Enabling bundled linux tools.
[00:29:12] Found bwa - /usr/local/bin/bwa
[00:29:12] Found bcftools - /usr/local/bin/bcftools
[00:29:12] Found samtools - /usr/local/bin/samtools
[00:29:12] Found java - /usr/local/bin/java
[00:29:12] Found snpEff - /usr/local/bin/snpEff
[00:29:12] Found samclip - /usr/local/bin/samclip
[00:29:12] Found seqtk - /usr/local/bin/seqtk
[00:29:12] Found parallel - /usr/local/bin/parallel
[00:29:12] Found freebayes - /usr/local/bin/freebayes
[00:29:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:12] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:12] Found gzip - /bin/gzip
[00:29:12] Found vt - /usr/local/bin/vt
[00:29:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:27:18] This is snippy 4.6.0Show full stderr[00:27:18] This is snippy 4.6.0
[00:27:18] Written by Torsten Seemann
[00:27:18] Obtained from https://github.com/tseemann/snippy
[00:27:18] Detected operating system: linux
[00:27:18] Enabling bundled linux tools.
[00:27:18] Found bwa - /usr/local/bin/bwa
[00:27:18] Found bcftools - /usr/local/bin/bcftools
[00:27:18] Found samtools - /usr/local/bin/samtools
[00:27:18] Found java - /usr/local/bin/java
[00:27:18] Found snpEff - /usr/local/bin/snpEff
[00:27:18] Found samclip - /usr/local/bin/samclip
[00:27:18] Found seqtk - /usr/local/bin/seqtk
[00:27:18] Found parallel - /usr/local/bin/parallel
[00:27:19] Found freebayes - /usr/local/bin/freebayes
[00:27:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:27:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:27:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:27:19] Found vcfuniq - /usr/local/bin/vcfuniq
[00:27:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:27:19] Found gzip - /bin/gzip
[00:27:19] Found vt - /usr/local/bin/vt
[00:27:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:27:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:27:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:27:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:27:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:27:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:27:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:27:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:26:57] This is snippy 4.6.0Show full stderr[00:26:57] This is snippy 4.6.0
[00:26:57] Written by Torsten Seemann
[00:26:57] Obtained from https://github.com/tseemann/snippy
[00:26:57] Detected operating system: linux
[00:26:57] Enabling bundled linux tools.
[00:26:57] Found bwa - /usr/local/bin/bwa
[00:26:57] Found bcftools - /usr/local/bin/bcftools
[00:26:57] Found samtools - /usr/local/bin/samtools
[00:26:57] Found java - /usr/local/bin/java
[00:26:57] Found snpEff - /usr/local/bin/snpEff
[00:26:57] Found samclip - /usr/local/bin/samclip
[00:26:57] Found seqtk - /usr/local/bin/seqtk
[00:26:57] Found parallel - /usr/local/bin/parallel
[00:26:57] Found freebayes - /usr/local/bin/freebayes
[00:26:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:58] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:58] Found gzip - /bin/gzip
[00:26:58] Found vt - /usr/local/bin/vt
[00:26:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:28:22] This is snippy 4.6.0Show full stderr[00:28:22] This is snippy 4.6.0
[00:28:22] Written by Torsten Seemann
[00:28:22] Obtained from https://github.com/tseemann/snippy
[00:28:22] Detected operating system: linux
[00:28:22] Enabling bundled linux tools.
[00:28:22] Found bwa - /usr/local/bin/bwa
[00:28:22] Found bcftools - /usr/local/bin/bcftools
[00:28:22] Found samtools - /usr/local/bin/samtools
[00:28:22] Found java - /usr/local/bin/java
[00:28:22] Found snpEff - /usr/local/bin/snpEff
[00:28:22] Found samclip - /usr/local/bin/samclip
[00:28:22] Found seqtk - /usr/local/bin/seqtk
[00:28:22] Found parallel - /usr/local/bin/parallel
[00:28:22] Found freebayes - /usr/local/bin/freebayes
[00:28:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:28:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:28:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:28:22] Found vcfuniq - /usr/local/bin/vcfuniq
[00:28:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:28:22] Found gzip - /bin/gzip
[00:28:22] Found vt - /usr/local/bin/vt
[00:28:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:28:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:28:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:28:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:28:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:28:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:28:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:28:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:28:24] This is snippy 4.6.0Show full stderr[00:28:24] This is snippy 4.6.0
[00:28:24] Written by Torsten Seemann
[00:28:24] Obtained from https://github.com/tseemann/snippy
[00:28:24] Detected operating system: linux
[00:28:24] Enabling bundled linux tools.
[00:28:24] Found bwa - /usr/local/bin/bwa
[00:28:24] Found bcftools - /usr/local/bin/bcftools
[00:28:24] Found samtools - /usr/local/bin/samtools
[00:28:24] Found java - /usr/local/bin/java
[00:28:24] Found snpEff - /usr/local/bin/snpEff
[00:28:24] Found samclip - /usr/local/bin/samclip
[00:28:24] Found seqtk - /usr/local/bin/seqtk
[00:28:24] Found parallel - /usr/local/bin/parallel
[00:28:24] Found freebayes - /usr/local/bin/freebayes
[00:28:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:28:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:28:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:28:25] Found vcfuniq - /usr/local/bin/vcfuniq
[00:28:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:28:25] Found gzip - /bin/gzip
[00:28:25] Found vt - /usr/local/bin/vt
[00:28:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:28:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:28:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:28:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:28:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:28:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:28:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:28:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:23:42] This is snippy 4.6.0Show full stderr[00:23:42] This is snippy 4.6.0
[00:23:42] Written by Torsten Seemann
[00:23:42] Obtained from https://github.com/tseemann/snippy
[00:23:42] Detected operating system: linux
[00:23:42] Enabling bundled linux tools.
[00:23:42] Found bwa - /usr/local/bin/bwa
[00:23:42] Found bcftools - /usr/local/bin/bcftools
[00:23:42] Found samtools - /usr/local/bin/samtools
[00:23:42] Found java - /usr/local/bin/java
[00:23:42] Found snpEff - /usr/local/bin/snpEff
[00:23:42] Found samclip - /usr/local/bin/samclip
[00:23:42] Found seqtk - /usr/local/bin/seqtk
[00:23:42] Found parallel - /usr/local/bin/parallel
[00:23:42] Found freebayes - /usr/local/bin/freebayes
[00:23:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:42] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:42] Found gzip - /bin/gzip
[00:23:42] Found vt - /usr/local/bin/vt
[00:23:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:23:44] This is snippy 4.6.0Show full stderr[00:23:44] This is snippy 4.6.0
[00:23:44] Written by Torsten Seemann
[00:23:44] Obtained from https://github.com/tseemann/snippy
[00:23:44] Detected operating system: linux
[00:23:44] Enabling bundled linux tools.
[00:23:44] Found bwa - /usr/local/bin/bwa
[00:23:44] Found bcftools - /usr/local/bin/bcftools
[00:23:44] Found samtools - /usr/local/bin/samtools
[00:23:44] Found java - /usr/local/bin/java
[00:23:44] Found snpEff - /usr/local/bin/snpEff
[00:23:44] Found samclip - /usr/local/bin/samclip
[00:23:44] Found seqtk - /usr/local/bin/seqtk
[00:23:44] Found parallel - /usr/local/bin/parallel
[00:23:44] Found freebayes - /usr/local/bin/freebayes
[00:23:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:23:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:23:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:23:44] Found vcfuniq - /usr/local/bin/vcfuniq
[00:23:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:23:44] Found gzip - /bin/gzip
[00:23:44] Found vt - /usr/local/bin/vt
[00:23:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:23:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:23:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:23:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:23:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:23:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:23:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:23:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:24:14] This is snippy 4.6.0Show full stderr[00:24:14] This is snippy 4.6.0
[00:24:14] Written by Torsten Seemann
[00:24:14] Obtained from https://github.com/tseemann/snippy
[00:24:14] Detected operating system: linux
[00:24:14] Enabling bundled linux tools.
[00:24:14] Found bwa - /usr/local/bin/bwa
[00:24:14] Found bcftools - /usr/local/bin/bcftools
[00:24:14] Found samtools - /usr/local/bin/samtools
[00:24:14] Found java - /usr/local/bin/java
[00:24:14] Found snpEff - /usr/local/bin/snpEff
[00:24:14] Found samclip - /usr/local/bin/samclip
[00:24:14] Found seqtk - /usr/local/bin/seqtk
[00:24:14] Found parallel - /usr/local/bin/parallel
[00:24:14] Found freebayes - /usr/local/bin/freebayes
[00:24:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:24:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:24:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:24:14] Found vcfuniq - /usr/local/bin/vcfuniq
[00:24:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:24:14] Found gzip - /bin/gzip
[00:24:15] Found vt - /usr/local/bin/vt
[00:24:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:24:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:24:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:24:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:24:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:24:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:24:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:24:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:11] This is snippy 4.6.0Show full stderr[00:29:11] This is snippy 4.6.0
[00:29:11] Written by Torsten Seemann
[00:29:11] Obtained from https://github.com/tseemann/snippy
[00:29:11] Detected operating system: linux
[00:29:11] Enabling bundled linux tools.
[00:29:11] Found bwa - /usr/local/bin/bwa
[00:29:12] Found bcftools - /usr/local/bin/bcftools
[00:29:12] Found samtools - /usr/local/bin/samtools
[00:29:12] Found java - /usr/local/bin/java
[00:29:12] Found snpEff - /usr/local/bin/snpEff
[00:29:12] Found samclip - /usr/local/bin/samclip
[00:29:12] Found seqtk - /usr/local/bin/seqtk
[00:29:12] Found parallel - /usr/local/bin/parallel
[00:29:12] Found freebayes - /usr/local/bin/freebayes
[00:29:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:12] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:12] Found gzip - /bin/gzip
[00:29:12] Found vt - /usr/local/bin/vt
[00:29:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:27:39] This is snippy 4.6.0Show full stderr[00:27:39] This is snippy 4.6.0
[00:27:39] Written by Torsten Seemann
[00:27:39] Obtained from https://github.com/tseemann/snippy
[00:27:39] Detected operating system: linux
[00:27:39] Enabling bundled linux tools.
[00:27:39] Found bwa - /usr/local/bin/bwa
[00:27:39] Found bcftools - /usr/local/bin/bcftools
[00:27:39] Found samtools - /usr/local/bin/samtools
[00:27:39] Found java - /usr/local/bin/java
[00:27:39] Found snpEff - /usr/local/bin/snpEff
[00:27:39] Found samclip - /usr/local/bin/samclip
[00:27:39] Found seqtk - /usr/local/bin/seqtk
[00:27:39] Found parallel - /usr/local/bin/parallel
[00:27:39] Found freebayes - /usr/local/bin/freebayes
[00:27:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:27:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:27:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:27:39] Found vcfuniq - /usr/local/bin/vcfuniq
[00:27:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:27:39] Found gzip - /bin/gzip
[00:27:40] Found vt - /usr/local/bin/vt
[00:27:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:27:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:27:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:27:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:27:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:27:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:27:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:27:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:28:13] This is snippy 4.6.0Show full stderr[00:28:13] This is snippy 4.6.0
[00:28:13] Written by Torsten Seemann
[00:28:13] Obtained from https://github.com/tseemann/snippy
[00:28:13] Detected operating system: linux
[00:28:13] Enabling bundled linux tools.
[00:28:13] Found bwa - /usr/local/bin/bwa
[00:28:13] Found bcftools - /usr/local/bin/bcftools
[00:28:13] Found samtools - /usr/local/bin/samtools
[00:28:13] Found java - /usr/local/bin/java
[00:28:13] Found snpEff - /usr/local/bin/snpEff
[00:28:13] Found samclip - /usr/local/bin/samclip
[00:28:13] Found seqtk - /usr/local/bin/seqtk
[00:28:13] Found parallel - /usr/local/bin/parallel
[00:28:13] Found freebayes - /usr/local/bin/freebayes
[00:28:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:28:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:28:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:28:13] Found vcfuniq - /usr/local/bin/vcfuniq
[00:28:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:28:13] Found gzip - /bin/gzip
[00:28:13] Found vt - /usr/local/bin/vt
[00:28:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:28:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:28:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:28:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:28:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:28:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:28:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:28:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:41:15] This is snippy 4.6.0Show full stderr[00:41:15] This is snippy 4.6.0
[00:41:15] Written by Torsten Seemann
[00:41:15] Obtained from https://github.com/tseemann/snippy
[00:41:15] Detected operating system: linux
[00:41:15] Enabling bundled linux tools.
[00:41:15] Found bwa - /usr/local/bin/bwa
[00:41:15] Found bcftools - /usr/local/bin/bcftools
[00:41:15] Found samtools - /usr/local/bin/samtools
[00:41:15] Found java - /usr/local/bin/java
[00:41:15] Found snpEff - /usr/local/bin/snpEff
[00:41:15] Found samclip - /usr/local/bin/samclip
[00:41:15] Found seqtk - /usr/local/bin/seqtk
[00:41:15] Found parallel - /usr/local/bin/parallel
[00:41:15] Found freebayes - /usr/local/bin/freebayes
[00:41:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:41:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:41:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:41:15] Found vcfuniq - /usr/local/bin/vcfuniq
[00:41:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:41:15] Found gzip - /bin/gzip
[00:41:15] Found vt - /usr/local/bin/vt
[00:41:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:41:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:41:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:41:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:41:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:41:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:41:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:41:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:30:48] This is snippy 4.6.0Show full stderr[00:30:48] This is snippy 4.6.0
[00:30:48] Written by Torsten Seemann
[00:30:48] Obtained from https://github.com/tseemann/snippy
[00:30:48] Detected operating system: linux
[00:30:48] Enabling bundled linux tools.
[00:30:48] Found bwa - /usr/local/bin/bwa
[00:30:48] Found bcftools - /usr/local/bin/bcftools
[00:30:48] Found samtools - /usr/local/bin/samtools
[00:30:48] Found java - /usr/local/bin/java
[00:30:48] Found snpEff - /usr/local/bin/snpEff
[00:30:48] Found samclip - /usr/local/bin/samclip
[00:30:48] Found seqtk - /usr/local/bin/seqtk
[00:30:48] Found parallel - /usr/local/bin/parallel
[00:30:48] Found freebayes - /usr/local/bin/freebayes
[00:30:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:30:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:30:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:30:48] Found vcfuniq - /usr/local/bin/vcfuniq
[00:30:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:30:48] Found gzip - /bin/gzip
[00:30:48] Found vt - /usr/local/bin/vt
[00:30:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:30:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:30:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:30:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:30:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:30:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:30:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:30:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:21] This is snippy 4.6.0Show full stderr[00:31:21] This is snippy 4.6.0
[00:31:21] Written by Torsten Seemann
[00:31:21] Obtained from https://github.com/tseemann/snippy
[00:31:21] Detected operating system: linux
[00:31:21] Enabling bundled linux tools.
[00:31:21] Found bwa - /usr/local/bin/bwa
[00:31:21] Found bcftools - /usr/local/bin/bcftools
[00:31:21] Found samtools - /usr/local/bin/samtools
[00:31:21] Found java - /usr/local/bin/java
[00:31:21] Found snpEff - /usr/local/bin/snpEff
[00:31:21] Found samclip - /usr/local/bin/samclip
[00:31:21] Found seqtk - /usr/local/bin/seqtk
[00:31:21] Found parallel - /usr/local/bin/parallel
[00:31:21] Found freebayes - /usr/local/bin/freebayes
[00:31:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:21] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:21] Found gzip - /bin/gzip
[00:31:21] Found vt - /usr/local/bin/vt
[00:31:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:42] This is snippy 4.6.0Show full stderr[00:29:42] This is snippy 4.6.0
[00:29:42] Written by Torsten Seemann
[00:29:42] Obtained from https://github.com/tseemann/snippy
[00:29:42] Detected operating system: linux
[00:29:42] Enabling bundled linux tools.
[00:29:42] Found bwa - /usr/local/bin/bwa
[00:29:42] Found bcftools - /usr/local/bin/bcftools
[00:29:42] Found samtools - /usr/local/bin/samtools
[00:29:42] Found java - /usr/local/bin/java
[00:29:42] Found snpEff - /usr/local/bin/snpEff
[00:29:42] Found samclip - /usr/local/bin/samclip
[00:29:42] Found seqtk - /usr/local/bin/seqtk
[00:29:42] Found parallel - /usr/local/bin/parallel
[00:29:42] Found freebayes - /usr/local/bin/freebayes
[00:29:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:42] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:42] Found gzip - /bin/gzip
[00:29:42] Found vt - /usr/local/bin/vt
[00:29:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:30:57] This is snippy 4.6.0Show full stderr[00:30:57] This is snippy 4.6.0
[00:30:57] Written by Torsten Seemann
[00:30:57] Obtained from https://github.com/tseemann/snippy
[00:30:57] Detected operating system: linux
[00:30:57] Enabling bundled linux tools.
[00:30:57] Found bwa - /usr/local/bin/bwa
[00:30:57] Found bcftools - /usr/local/bin/bcftools
[00:30:57] Found samtools - /usr/local/bin/samtools
[00:30:57] Found java - /usr/local/bin/java
[00:30:57] Found snpEff - /usr/local/bin/snpEff
[00:30:57] Found samclip - /usr/local/bin/samclip
[00:30:57] Found seqtk - /usr/local/bin/seqtk
[00:30:57] Found parallel - /usr/local/bin/parallel
[00:30:57] Found freebayes - /usr/local/bin/freebayes
[00:30:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:30:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:30:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:30:57] Found vcfuniq - /usr/local/bin/vcfuniq
[00:30:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:30:57] Found gzip - /bin/gzip
[00:30:57] Found vt - /usr/local/bin/vt
[00:30:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:30:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:30:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:30:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:30:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:30:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:30:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:30:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:39] This is snippy 4.6.0Show full stderr[00:31:39] This is snippy 4.6.0
[00:31:39] Written by Torsten Seemann
[00:31:39] Obtained from https://github.com/tseemann/snippy
[00:31:39] Detected operating system: linux
[00:31:39] Enabling bundled linux tools.
[00:31:39] Found bwa - /usr/local/bin/bwa
[00:31:39] Found bcftools - /usr/local/bin/bcftools
[00:31:39] Found samtools - /usr/local/bin/samtools
[00:31:39] Found java - /usr/local/bin/java
[00:31:39] Found snpEff - /usr/local/bin/snpEff
[00:31:39] Found samclip - /usr/local/bin/samclip
[00:31:39] Found seqtk - /usr/local/bin/seqtk
[00:31:39] Found parallel - /usr/local/bin/parallel
[00:31:39] Found freebayes - /usr/local/bin/freebayes
[00:31:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:39] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:39] Found gzip - /bin/gzip
[00:31:39] Found vt - /usr/local/bin/vt
[00:31:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:32:54] This is snippy 4.6.0Show full stderr[00:32:54] This is snippy 4.6.0
[00:32:54] Written by Torsten Seemann
[00:32:54] Obtained from https://github.com/tseemann/snippy
[00:32:54] Detected operating system: linux
[00:32:54] Enabling bundled linux tools.
[00:32:54] Found bwa - /usr/local/bin/bwa
[00:32:54] Found bcftools - /usr/local/bin/bcftools
[00:32:54] Found samtools - /usr/local/bin/samtools
[00:32:54] Found java - /usr/local/bin/java
[00:32:54] Found snpEff - /usr/local/bin/snpEff
[00:32:54] Found samclip - /usr/local/bin/samclip
[00:32:54] Found seqtk - /usr/local/bin/seqtk
[00:32:54] Found parallel - /usr/local/bin/parallel
[00:32:54] Found freebayes - /usr/local/bin/freebayes
[00:32:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:32:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:32:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:32:54] Found vcfuniq - /usr/local/bin/vcfuniq
[00:32:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:32:54] Found gzip - /bin/gzip
[00:32:54] Found vt - /usr/local/bin/vt
[00:32:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:32:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:32:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:32:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:32:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:32:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:32:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:32:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:48:05] This is snippy 4.6.0Show full stderr[00:48:05] This is snippy 4.6.0
[00:48:05] Written by Torsten Seemann
[00:48:05] Obtained from https://github.com/tseemann/snippy
[00:48:05] Detected operating system: linux
[00:48:05] Enabling bundled linux tools.
[00:48:05] Found bwa - /usr/local/bin/bwa
[00:48:05] Found bcftools - /usr/local/bin/bcftools
[00:48:05] Found samtools - /usr/local/bin/samtools
[00:48:05] Found java - /usr/local/bin/java
[00:48:05] Found snpEff - /usr/local/bin/snpEff
[00:48:05] Found samclip - /usr/local/bin/samclip
[00:48:05] Found seqtk - /usr/local/bin/seqtk
[00:48:05] Found parallel - /usr/local/bin/parallel
[00:48:05] Found freebayes - /usr/local/bin/freebayes
[00:48:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:48:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:48:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:48:05] Found vcfuniq - /usr/local/bin/vcfuniq
[00:48:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:48:05] Found gzip - /bin/gzip
[00:48:05] Found vt - /usr/local/bin/vt
[00:48:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:48:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:48:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:48:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:48:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:48:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:48:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:48:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:06:25] This is snippy 4.6.0Show full stderr[01:06:25] This is snippy 4.6.0
[01:06:25] Written by Torsten Seemann
[01:06:25] Obtained from https://github.com/tseemann/snippy
[01:06:25] Detected operating system: linux
[01:06:25] Enabling bundled linux tools.
[01:06:25] Found bwa - /usr/local/bin/bwa
[01:06:25] Found bcftools - /usr/local/bin/bcftools
[01:06:25] Found samtools - /usr/local/bin/samtools
[01:06:25] Found java - /usr/local/bin/java
[01:06:25] Found snpEff - /usr/local/bin/snpEff
[01:06:25] Found samclip - /usr/local/bin/samclip
[01:06:25] Found seqtk - /usr/local/bin/seqtk
[01:06:25] Found parallel - /usr/local/bin/parallel
[01:06:25] Found freebayes - /usr/local/bin/freebayes
[01:06:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:06:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:06:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:06:25] Found vcfuniq - /usr/local/bin/vcfuniq
[01:06:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:06:25] Found gzip - /bin/gzip
[01:06:25] Found vt - /usr/local/bin/vt
[01:06:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:06:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:06:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:06:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:06:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:06:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:06:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:06:26] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:34:48] This is snippy 4.6.0Show full stderr[00:34:48] This is snippy 4.6.0
[00:34:48] Written by Torsten Seemann
[00:34:48] Obtained from https://github.com/tseemann/snippy
[00:34:48] Detected operating system: linux
[00:34:48] Enabling bundled linux tools.
[00:34:48] Found bwa - /usr/local/bin/bwa
[00:34:48] Found bcftools - /usr/local/bin/bcftools
[00:34:48] Found samtools - /usr/local/bin/samtools
[00:34:48] Found java - /usr/local/bin/java
[00:34:48] Found snpEff - /usr/local/bin/snpEff
[00:34:48] Found samclip - /usr/local/bin/samclip
[00:34:48] Found seqtk - /usr/local/bin/seqtk
[00:34:48] Found parallel - /usr/local/bin/parallel
[00:34:48] Found freebayes - /usr/local/bin/freebayes
[00:34:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:34:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:34:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:34:48] Found vcfuniq - /usr/local/bin/vcfuniq
[00:34:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:34:48] Found gzip - /bin/gzip
[00:34:48] Found vt - /usr/local/bin/vt
[00:34:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:34:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:34:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:34:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:34:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:34:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:34:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:34:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:35:24] This is snippy 4.6.0Show full stderr[00:35:24] This is snippy 4.6.0
[00:35:24] Written by Torsten Seemann
[00:35:24] Obtained from https://github.com/tseemann/snippy
[00:35:24] Detected operating system: linux
[00:35:24] Enabling bundled linux tools.
[00:35:24] Found bwa - /usr/local/bin/bwa
[00:35:24] Found bcftools - /usr/local/bin/bcftools
[00:35:24] Found samtools - /usr/local/bin/samtools
[00:35:24] Found java - /usr/local/bin/java
[00:35:24] Found snpEff - /usr/local/bin/snpEff
[00:35:24] Found samclip - /usr/local/bin/samclip
[00:35:24] Found seqtk - /usr/local/bin/seqtk
[00:35:24] Found parallel - /usr/local/bin/parallel
[00:35:24] Found freebayes - /usr/local/bin/freebayes
[00:35:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:35:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:35:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:35:24] Found vcfuniq - /usr/local/bin/vcfuniq
[00:35:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:35:24] Found gzip - /bin/gzip
[00:35:24] Found vt - /usr/local/bin/vt
[00:35:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:35:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:35:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:35:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:35:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:35:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:35:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:35:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:44:57] This is snippy 4.6.0Show full stderr[00:44:57] This is snippy 4.6.0
[00:44:57] Written by Torsten Seemann
[00:44:57] Obtained from https://github.com/tseemann/snippy
[00:44:57] Detected operating system: linux
[00:44:57] Enabling bundled linux tools.
[00:44:57] Found bwa - /usr/local/bin/bwa
[00:44:57] Found bcftools - /usr/local/bin/bcftools
[00:44:57] Found samtools - /usr/local/bin/samtools
[00:44:57] Found java - /usr/local/bin/java
[00:44:57] Found snpEff - /usr/local/bin/snpEff
[00:44:57] Found samclip - /usr/local/bin/samclip
[00:44:57] Found seqtk - /usr/local/bin/seqtk
[00:44:57] Found parallel - /usr/local/bin/parallel
[00:44:57] Found freebayes - /usr/local/bin/freebayes
[00:44:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:44:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:44:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:44:57] Found vcfuniq - /usr/local/bin/vcfuniq
[00:44:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:44:57] Found gzip - /bin/gzip
[00:44:57] Found vt - /usr/local/bin/vt
[00:44:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:44:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:44:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:44:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:44:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:44:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:44:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:44:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:47:37] This is snippy 4.6.0Show full stderr[00:47:37] This is snippy 4.6.0
[00:47:37] Written by Torsten Seemann
[00:47:37] Obtained from https://github.com/tseemann/snippy
[00:47:37] Detected operating system: linux
[00:47:37] Enabling bundled linux tools.
[00:47:37] Found bwa - /usr/local/bin/bwa
[00:47:37] Found bcftools - /usr/local/bin/bcftools
[00:47:37] Found samtools - /usr/local/bin/samtools
[00:47:37] Found java - /usr/local/bin/java
[00:47:37] Found snpEff - /usr/local/bin/snpEff
[00:47:37] Found samclip - /usr/local/bin/samclip
[00:47:37] Found seqtk - /usr/local/bin/seqtk
[00:47:37] Found parallel - /usr/local/bin/parallel
[00:47:37] Found freebayes - /usr/local/bin/freebayes
[00:47:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:47:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:47:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:47:37] Found vcfuniq - /usr/local/bin/vcfuniq
[00:47:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:47:37] Found gzip - /bin/gzip
[00:47:37] Found vt - /usr/local/bin/vt
[00:47:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:47:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:47:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:47:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:47:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:47:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:47:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:47:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:51:55] This is snippy 4.6.0Show full stderr[00:51:55] This is snippy 4.6.0
[00:51:55] Written by Torsten Seemann
[00:51:55] Obtained from https://github.com/tseemann/snippy
[00:51:55] Detected operating system: linux
[00:51:55] Enabling bundled linux tools.
[00:51:55] Found bwa - /usr/local/bin/bwa
[00:51:55] Found bcftools - /usr/local/bin/bcftools
[00:51:55] Found samtools - /usr/local/bin/samtools
[00:51:55] Found java - /usr/local/bin/java
[00:51:55] Found snpEff - /usr/local/bin/snpEff
[00:51:55] Found samclip - /usr/local/bin/samclip
[00:51:55] Found seqtk - /usr/local/bin/seqtk
[00:51:55] Found parallel - /usr/local/bin/parallel
[00:51:55] Found freebayes - /usr/local/bin/freebayes
[00:51:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:51:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:51:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:51:55] Found vcfuniq - /usr/local/bin/vcfuniq
[00:51:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:51:55] Found gzip - /bin/gzip
[00:51:55] Found vt - /usr/local/bin/vt
[00:51:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:51:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:51:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:51:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:51:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:51:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:51:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:51:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:06:54] This is snippy 4.6.0Show full stderr[01:06:54] This is snippy 4.6.0
[01:06:54] Written by Torsten Seemann
[01:06:54] Obtained from https://github.com/tseemann/snippy
[01:06:54] Detected operating system: linux
[01:06:54] Enabling bundled linux tools.
[01:06:54] Found bwa - /usr/local/bin/bwa
[01:06:54] Found bcftools - /usr/local/bin/bcftools
[01:06:54] Found samtools - /usr/local/bin/samtools
[01:06:54] Found java - /usr/local/bin/java
[01:06:54] Found snpEff - /usr/local/bin/snpEff
[01:06:54] Found samclip - /usr/local/bin/samclip
[01:06:54] Found seqtk - /usr/local/bin/seqtk
[01:06:54] Found parallel - /usr/local/bin/parallel
[01:06:54] Found freebayes - /usr/local/bin/freebayes
[01:06:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:06:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:06:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:06:54] Found vcfuniq - /usr/local/bin/vcfuniq
[01:06:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:06:54] Found gzip - /bin/gzip
[01:06:54] Found vt - /usr/local/bin/vt
[01:06:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:06:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:06:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:06:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:06:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:06:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:06:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:06:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:59:31] This is snippy 4.6.0Show full stderr[00:59:31] This is snippy 4.6.0
[00:59:31] Written by Torsten Seemann
[00:59:31] Obtained from https://github.com/tseemann/snippy
[00:59:31] Detected operating system: linux
[00:59:31] Enabling bundled linux tools.
[00:59:31] Found bwa - /usr/local/bin/bwa
[00:59:31] Found bcftools - /usr/local/bin/bcftools
[00:59:31] Found samtools - /usr/local/bin/samtools
[00:59:31] Found java - /usr/local/bin/java
[00:59:31] Found snpEff - /usr/local/bin/snpEff
[00:59:31] Found samclip - /usr/local/bin/samclip
[00:59:31] Found seqtk - /usr/local/bin/seqtk
[00:59:31] Found parallel - /usr/local/bin/parallel
[00:59:31] Found freebayes - /usr/local/bin/freebayes
[00:59:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:59:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:59:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:59:31] Found vcfuniq - /usr/local/bin/vcfuniq
[00:59:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:59:31] Found gzip - /bin/gzip
[00:59:31] Found vt - /usr/local/bin/vt
[00:59:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:59:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:59:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:59:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:59:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:59:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:59:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:59:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:30:14] This is snippy 4.6.0Show full stderr[00:30:14] This is snippy 4.6.0
[00:30:14] Written by Torsten Seemann
[00:30:14] Obtained from https://github.com/tseemann/snippy
[00:30:14] Detected operating system: linux
[00:30:14] Enabling bundled linux tools.
[00:30:14] Found bwa - /usr/local/bin/bwa
[00:30:14] Found bcftools - /usr/local/bin/bcftools
[00:30:14] Found samtools - /usr/local/bin/samtools
[00:30:14] Found java - /usr/local/bin/java
[00:30:14] Found snpEff - /usr/local/bin/snpEff
[00:30:14] Found samclip - /usr/local/bin/samclip
[00:30:14] Found seqtk - /usr/local/bin/seqtk
[00:30:14] Found parallel - /usr/local/bin/parallel
[00:30:14] Found freebayes - /usr/local/bin/freebayes
[00:30:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:30:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:30:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:30:14] Found vcfuniq - /usr/local/bin/vcfuniq
[00:30:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:30:14] Found gzip - /bin/gzip
[00:30:14] Found vt - /usr/local/bin/vt
[00:30:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:30:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:30:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:30:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:30:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:30:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:30:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:30:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:30:33] This is snippy 4.6.0Show full stderr[00:30:33] This is snippy 4.6.0
[00:30:33] Written by Torsten Seemann
[00:30:33] Obtained from https://github.com/tseemann/snippy
[00:30:33] Detected operating system: linux
[00:30:33] Enabling bundled linux tools.
[00:30:33] Found bwa - /usr/local/bin/bwa
[00:30:33] Found bcftools - /usr/local/bin/bcftools
[00:30:33] Found samtools - /usr/local/bin/samtools
[00:30:33] Found java - /usr/local/bin/java
[00:30:33] Found snpEff - /usr/local/bin/snpEff
[00:30:33] Found samclip - /usr/local/bin/samclip
[00:30:33] Found seqtk - /usr/local/bin/seqtk
[00:30:33] Found parallel - /usr/local/bin/parallel
[00:30:33] Found freebayes - /usr/local/bin/freebayes
[00:30:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:30:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:30:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:30:33] Found vcfuniq - /usr/local/bin/vcfuniq
[00:30:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:30:33] Found gzip - /bin/gzip
[00:30:33] Found vt - /usr/local/bin/vt
[00:30:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:30:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:30:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:30:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:30:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:30:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:30:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:30:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:14] This is snippy 4.6.0Show full stderr[00:31:14] This is snippy 4.6.0
[00:31:14] Written by Torsten Seemann
[00:31:14] Obtained from https://github.com/tseemann/snippy
[00:31:14] Detected operating system: linux
[00:31:14] Enabling bundled linux tools.
[00:31:14] Found bwa - /usr/local/bin/bwa
[00:31:14] Found bcftools - /usr/local/bin/bcftools
[00:31:14] Found samtools - /usr/local/bin/samtools
[00:31:14] Found java - /usr/local/bin/java
[00:31:14] Found snpEff - /usr/local/bin/snpEff
[00:31:14] Found samclip - /usr/local/bin/samclip
[00:31:14] Found seqtk - /usr/local/bin/seqtk
[00:31:14] Found parallel - /usr/local/bin/parallel
[00:31:14] Found freebayes - /usr/local/bin/freebayes
[00:31:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:14] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:14] Found gzip - /bin/gzip
[00:31:14] Found vt - /usr/local/bin/vt
[00:31:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:15] This is snippy 4.6.0Show full stderr[00:31:15] This is snippy 4.6.0
[00:31:15] Written by Torsten Seemann
[00:31:15] Obtained from https://github.com/tseemann/snippy
[00:31:15] Detected operating system: linux
[00:31:15] Enabling bundled linux tools.
[00:31:15] Found bwa - /usr/local/bin/bwa
[00:31:15] Found bcftools - /usr/local/bin/bcftools
[00:31:15] Found samtools - /usr/local/bin/samtools
[00:31:15] Found java - /usr/local/bin/java
[00:31:15] Found snpEff - /usr/local/bin/snpEff
[00:31:15] Found samclip - /usr/local/bin/samclip
[00:31:15] Found seqtk - /usr/local/bin/seqtk
[00:31:15] Found parallel - /usr/local/bin/parallel
[00:31:15] Found freebayes - /usr/local/bin/freebayes
[00:31:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:15] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:15] Found gzip - /bin/gzip
[00:31:15] Found vt - /usr/local/bin/vt
[00:31:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:24] This is snippy 4.6.0Show full stderr[00:31:24] This is snippy 4.6.0
[00:31:24] Written by Torsten Seemann
[00:31:24] Obtained from https://github.com/tseemann/snippy
[00:31:24] Detected operating system: linux
[00:31:24] Enabling bundled linux tools.
[00:31:24] Found bwa - /usr/local/bin/bwa
[00:31:24] Found bcftools - /usr/local/bin/bcftools
[00:31:24] Found samtools - /usr/local/bin/samtools
[00:31:24] Found java - /usr/local/bin/java
[00:31:24] Found snpEff - /usr/local/bin/snpEff
[00:31:24] Found samclip - /usr/local/bin/samclip
[00:31:24] Found seqtk - /usr/local/bin/seqtk
[00:31:24] Found parallel - /usr/local/bin/parallel
[00:31:24] Found freebayes - /usr/local/bin/freebayes
[00:31:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:24] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:24] Found gzip - /bin/gzip
[00:31:24] Found vt - /usr/local/bin/vt
[00:31:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:33:00] This is snippy 4.6.0Show full stderr[00:33:00] This is snippy 4.6.0
[00:33:00] Written by Torsten Seemann
[00:33:00] Obtained from https://github.com/tseemann/snippy
[00:33:00] Detected operating system: linux
[00:33:00] Enabling bundled linux tools.
[00:33:00] Found bwa - /usr/local/bin/bwa
[00:33:00] Found bcftools - /usr/local/bin/bcftools
[00:33:00] Found samtools - /usr/local/bin/samtools
[00:33:00] Found java - /usr/local/bin/java
[00:33:00] Found snpEff - /usr/local/bin/snpEff
[00:33:00] Found samclip - /usr/local/bin/samclip
[00:33:00] Found seqtk - /usr/local/bin/seqtk
[00:33:00] Found parallel - /usr/local/bin/parallel
[00:33:00] Found freebayes - /usr/local/bin/freebayes
[00:33:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:00] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:00] Found gzip - /bin/gzip
[00:33:00] Found vt - /usr/local/bin/vt
[00:33:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:58:36] This is snippy 4.6.0Show full stderr[00:58:36] This is snippy 4.6.0
[00:58:36] Written by Torsten Seemann
[00:58:36] Obtained from https://github.com/tseemann/snippy
[00:58:36] Detected operating system: linux
[00:58:36] Enabling bundled linux tools.
[00:58:36] Found bwa - /usr/local/bin/bwa
[00:58:36] Found bcftools - /usr/local/bin/bcftools
[00:58:36] Found samtools - /usr/local/bin/samtools
[00:58:36] Found java - /usr/local/bin/java
[00:58:36] Found snpEff - /usr/local/bin/snpEff
[00:58:36] Found samclip - /usr/local/bin/samclip
[00:58:36] Found seqtk - /usr/local/bin/seqtk
[00:58:36] Found parallel - /usr/local/bin/parallel
[00:58:36] Found freebayes - /usr/local/bin/freebayes
[00:58:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:58:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:58:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:58:36] Found vcfuniq - /usr/local/bin/vcfuniq
[00:58:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:58:36] Found gzip - /bin/gzip
[00:58:36] Found vt - /usr/local/bin/vt
[00:58:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:58:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:58:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:58:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:58:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:58:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:58:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:58:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:26:04] This is snippy 4.6.0Show full stderr[00:26:04] This is snippy 4.6.0
[00:26:04] Written by Torsten Seemann
[00:26:04] Obtained from https://github.com/tseemann/snippy
[00:26:04] Detected operating system: linux
[00:26:04] Enabling bundled linux tools.
[00:26:04] Found bwa - /usr/local/bin/bwa
[00:26:04] Found bcftools - /usr/local/bin/bcftools
[00:26:04] Found samtools - /usr/local/bin/samtools
[00:26:04] Found java - /usr/local/bin/java
[00:26:04] Found snpEff - /usr/local/bin/snpEff
[00:26:04] Found samclip - /usr/local/bin/samclip
[00:26:04] Found seqtk - /usr/local/bin/seqtk
[00:26:04] Found parallel - /usr/local/bin/parallel
[00:26:04] Found freebayes - /usr/local/bin/freebayes
[00:26:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:04] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:04] Found gzip - /bin/gzip
[00:26:04] Found vt - /usr/local/bin/vt
[00:26:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:06] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:26:06] This is snippy 4.6.0Show full stderr[00:26:06] This is snippy 4.6.0
[00:26:06] Written by Torsten Seemann
[00:26:06] Obtained from https://github.com/tseemann/snippy
[00:26:06] Detected operating system: linux
[00:26:06] Enabling bundled linux tools.
[00:26:06] Found bwa - /usr/local/bin/bwa
[00:26:06] Found bcftools - /usr/local/bin/bcftools
[00:26:06] Found samtools - /usr/local/bin/samtools
[00:26:06] Found java - /usr/local/bin/java
[00:26:06] Found snpEff - /usr/local/bin/snpEff
[00:26:06] Found samclip - /usr/local/bin/samclip
[00:26:06] Found seqtk - /usr/local/bin/seqtk
[00:26:06] Found parallel - /usr/local/bin/parallel
[00:26:06] Found freebayes - /usr/local/bin/freebayes
[00:26:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:06] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:06] Found gzip - /bin/gzip
[00:26:06] Found vt - /usr/local/bin/vt
[00:26:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:26:24] This is snippy 4.6.0Show full stderr[00:26:24] This is snippy 4.6.0
[00:26:24] Written by Torsten Seemann
[00:26:24] Obtained from https://github.com/tseemann/snippy
[00:26:24] Detected operating system: linux
[00:26:24] Enabling bundled linux tools.
[00:26:24] Found bwa - /usr/local/bin/bwa
[00:26:24] Found bcftools - /usr/local/bin/bcftools
[00:26:24] Found samtools - /usr/local/bin/samtools
[00:26:24] Found java - /usr/local/bin/java
[00:26:24] Found snpEff - /usr/local/bin/snpEff
[00:26:24] Found samclip - /usr/local/bin/samclip
[00:26:24] Found seqtk - /usr/local/bin/seqtk
[00:26:24] Found parallel - /usr/local/bin/parallel
[00:26:24] Found freebayes - /usr/local/bin/freebayes
[00:26:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:26:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:26:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:26:24] Found vcfuniq - /usr/local/bin/vcfuniq
[00:26:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:26:24] Found gzip - /bin/gzip
[00:26:24] Found vt - /usr/local/bin/vt
[00:26:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:26:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:26:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:26:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:26:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:26:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:26:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:26:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:27:42] This is snippy 4.6.0Show full stderr[00:27:42] This is snippy 4.6.0
[00:27:42] Written by Torsten Seemann
[00:27:42] Obtained from https://github.com/tseemann/snippy
[00:27:42] Detected operating system: linux
[00:27:42] Enabling bundled linux tools.
[00:27:42] Found bwa - /usr/local/bin/bwa
[00:27:42] Found bcftools - /usr/local/bin/bcftools
[00:27:42] Found samtools - /usr/local/bin/samtools
[00:27:43] Found java - /usr/local/bin/java
[00:27:43] Found snpEff - /usr/local/bin/snpEff
[00:27:43] Found samclip - /usr/local/bin/samclip
[00:27:43] Found seqtk - /usr/local/bin/seqtk
[00:27:43] Found parallel - /usr/local/bin/parallel
[00:27:43] Found freebayes - /usr/local/bin/freebayes
[00:27:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:27:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:27:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:27:43] Found vcfuniq - /usr/local/bin/vcfuniq
[00:27:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:27:43] Found gzip - /bin/gzip
[00:27:43] Found vt - /usr/local/bin/vt
[00:27:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:27:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:27:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:27:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:27:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:27:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:27:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:27:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:27:58] This is snippy 4.6.0Show full stderr[00:27:58] This is snippy 4.6.0
[00:27:58] Written by Torsten Seemann
[00:27:58] Obtained from https://github.com/tseemann/snippy
[00:27:58] Detected operating system: linux
[00:27:58] Enabling bundled linux tools.
[00:27:58] Found bwa - /usr/local/bin/bwa
[00:27:58] Found bcftools - /usr/local/bin/bcftools
[00:27:58] Found samtools - /usr/local/bin/samtools
[00:27:58] Found java - /usr/local/bin/java
[00:27:58] Found snpEff - /usr/local/bin/snpEff
[00:27:58] Found samclip - /usr/local/bin/samclip
[00:27:58] Found seqtk - /usr/local/bin/seqtk
[00:27:58] Found parallel - /usr/local/bin/parallel
[00:27:58] Found freebayes - /usr/local/bin/freebayes
[00:27:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:27:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:27:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:27:58] Found vcfuniq - /usr/local/bin/vcfuniq
[00:27:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:27:58] Found gzip - /bin/gzip
[00:27:58] Found vt - /usr/local/bin/vt
[00:27:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:27:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:27:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:27:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:27:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:27:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:27:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:27:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:28:33] This is snippy 4.6.0Show full stderr[00:28:33] This is snippy 4.6.0
[00:28:33] Written by Torsten Seemann
[00:28:33] Obtained from https://github.com/tseemann/snippy
[00:28:33] Detected operating system: linux
[00:28:33] Enabling bundled linux tools.
[00:28:33] Found bwa - /usr/local/bin/bwa
[00:28:33] Found bcftools - /usr/local/bin/bcftools
[00:28:33] Found samtools - /usr/local/bin/samtools
[00:28:33] Found java - /usr/local/bin/java
[00:28:33] Found snpEff - /usr/local/bin/snpEff
[00:28:33] Found samclip - /usr/local/bin/samclip
[00:28:33] Found seqtk - /usr/local/bin/seqtk
[00:28:33] Found parallel - /usr/local/bin/parallel
[00:28:33] Found freebayes - /usr/local/bin/freebayes
[00:28:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:28:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:28:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:28:34] Found vcfuniq - /usr/local/bin/vcfuniq
[00:28:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:28:34] Found gzip - /bin/gzip
[00:28:34] Found vt - /usr/local/bin/vt
[00:28:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:28:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:28:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:28:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:28:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:28:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:28:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:28:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:28:50] This is snippy 4.6.0Show full stderr[00:28:50] This is snippy 4.6.0
[00:28:50] Written by Torsten Seemann
[00:28:50] Obtained from https://github.com/tseemann/snippy
[00:28:50] Detected operating system: linux
[00:28:50] Enabling bundled linux tools.
[00:28:50] Found bwa - /usr/local/bin/bwa
[00:28:50] Found bcftools - /usr/local/bin/bcftools
[00:28:50] Found samtools - /usr/local/bin/samtools
[00:28:50] Found java - /usr/local/bin/java
[00:28:50] Found snpEff - /usr/local/bin/snpEff
[00:28:50] Found samclip - /usr/local/bin/samclip
[00:28:50] Found seqtk - /usr/local/bin/seqtk
[00:28:50] Found parallel - /usr/local/bin/parallel
[00:28:50] Found freebayes - /usr/local/bin/freebayes
[00:28:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:28:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:28:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:28:51] Found vcfuniq - /usr/local/bin/vcfuniq
[00:28:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:28:51] Found gzip - /bin/gzip
[00:28:51] Found vt - /usr/local/bin/vt
[00:28:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:28:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:28:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:28:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:28:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:28:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:28:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:28:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:28:54] This is snippy 4.6.0Show full stderr[00:28:54] This is snippy 4.6.0
[00:28:54] Written by Torsten Seemann
[00:28:54] Obtained from https://github.com/tseemann/snippy
[00:28:54] Detected operating system: linux
[00:28:54] Enabling bundled linux tools.
[00:28:54] Found bwa - /usr/local/bin/bwa
[00:28:54] Found bcftools - /usr/local/bin/bcftools
[00:28:54] Found samtools - /usr/local/bin/samtools
[00:28:54] Found java - /usr/local/bin/java
[00:28:54] Found snpEff - /usr/local/bin/snpEff
[00:28:54] Found samclip - /usr/local/bin/samclip
[00:28:54] Found seqtk - /usr/local/bin/seqtk
[00:28:54] Found parallel - /usr/local/bin/parallel
[00:28:54] Found freebayes - /usr/local/bin/freebayes
[00:28:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:28:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:28:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:28:54] Found vcfuniq - /usr/local/bin/vcfuniq
[00:28:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:28:54] Found gzip - /bin/gzip
[00:28:54] Found vt - /usr/local/bin/vt
[00:28:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:28:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:28:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:28:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:28:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:28:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:28:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:28:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:28:57] This is snippy 4.6.0Show full stderr[00:28:57] This is snippy 4.6.0
[00:28:57] Written by Torsten Seemann
[00:28:57] Obtained from https://github.com/tseemann/snippy
[00:28:57] Detected operating system: linux
[00:28:57] Enabling bundled linux tools.
[00:28:57] Found bwa - /usr/local/bin/bwa
[00:28:57] Found bcftools - /usr/local/bin/bcftools
[00:28:57] Found samtools - /usr/local/bin/samtools
[00:28:57] Found java - /usr/local/bin/java
[00:28:57] Found snpEff - /usr/local/bin/snpEff
[00:28:57] Found samclip - /usr/local/bin/samclip
[00:28:57] Found seqtk - /usr/local/bin/seqtk
[00:28:57] Found parallel - /usr/local/bin/parallel
[00:28:57] Found freebayes - /usr/local/bin/freebayes
[00:28:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:28:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:28:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:28:57] Found vcfuniq - /usr/local/bin/vcfuniq
[00:28:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:28:57] Found gzip - /bin/gzip
[00:28:57] Found vt - /usr/local/bin/vt
[00:28:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:28:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:28:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:28:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:28:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:28:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:28:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:28:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:18] This is snippy 4.6.0Show full stderr[00:29:18] This is snippy 4.6.0
[00:29:18] Written by Torsten Seemann
[00:29:18] Obtained from https://github.com/tseemann/snippy
[00:29:18] Detected operating system: linux
[00:29:18] Enabling bundled linux tools.
[00:29:18] Found bwa - /usr/local/bin/bwa
[00:29:18] Found bcftools - /usr/local/bin/bcftools
[00:29:18] Found samtools - /usr/local/bin/samtools
[00:29:18] Found java - /usr/local/bin/java
[00:29:18] Found snpEff - /usr/local/bin/snpEff
[00:29:18] Found samclip - /usr/local/bin/samclip
[00:29:18] Found seqtk - /usr/local/bin/seqtk
[00:29:18] Found parallel - /usr/local/bin/parallel
[00:29:18] Found freebayes - /usr/local/bin/freebayes
[00:29:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:18] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:18] Found gzip - /bin/gzip
[00:29:18] Found vt - /usr/local/bin/vt
[00:29:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:21] This is snippy 4.6.0Show full stderr[00:29:21] This is snippy 4.6.0
[00:29:21] Written by Torsten Seemann
[00:29:21] Obtained from https://github.com/tseemann/snippy
[00:29:21] Detected operating system: linux
[00:29:21] Enabling bundled linux tools.
[00:29:21] Found bwa - /usr/local/bin/bwa
[00:29:21] Found bcftools - /usr/local/bin/bcftools
[00:29:21] Found samtools - /usr/local/bin/samtools
[00:29:21] Found java - /usr/local/bin/java
[00:29:21] Found snpEff - /usr/local/bin/snpEff
[00:29:21] Found samclip - /usr/local/bin/samclip
[00:29:21] Found seqtk - /usr/local/bin/seqtk
[00:29:21] Found parallel - /usr/local/bin/parallel
[00:29:21] Found freebayes - /usr/local/bin/freebayes
[00:29:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:21] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:21] Found gzip - /bin/gzip
[00:29:21] Found vt - /usr/local/bin/vt
[00:29:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:22] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:39] This is snippy 4.6.0Show full stderr[00:29:39] This is snippy 4.6.0
[00:29:39] Written by Torsten Seemann
[00:29:39] Obtained from https://github.com/tseemann/snippy
[00:29:39] Detected operating system: linux
[00:29:39] Enabling bundled linux tools.
[00:29:39] Found bwa - /usr/local/bin/bwa
[00:29:39] Found bcftools - /usr/local/bin/bcftools
[00:29:39] Found samtools - /usr/local/bin/samtools
[00:29:39] Found java - /usr/local/bin/java
[00:29:39] Found snpEff - /usr/local/bin/snpEff
[00:29:39] Found samclip - /usr/local/bin/samclip
[00:29:39] Found seqtk - /usr/local/bin/seqtk
[00:29:39] Found parallel - /usr/local/bin/parallel
[00:29:39] Found freebayes - /usr/local/bin/freebayes
[00:29:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:39] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:39] Found gzip - /bin/gzip
[00:29:39] Found vt - /usr/local/bin/vt
[00:29:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:53] This is snippy 4.6.0Show full stderr[00:29:53] This is snippy 4.6.0
[00:29:53] Written by Torsten Seemann
[00:29:53] Obtained from https://github.com/tseemann/snippy
[00:29:53] Detected operating system: linux
[00:29:53] Enabling bundled linux tools.
[00:29:53] Found bwa - /usr/local/bin/bwa
[00:29:54] Found bcftools - /usr/local/bin/bcftools
[00:29:54] Found samtools - /usr/local/bin/samtools
[00:29:54] Found java - /usr/local/bin/java
[00:29:54] Found snpEff - /usr/local/bin/snpEff
[00:29:54] Found samclip - /usr/local/bin/samclip
[00:29:54] Found seqtk - /usr/local/bin/seqtk
[00:29:54] Found parallel - /usr/local/bin/parallel
[00:29:54] Found freebayes - /usr/local/bin/freebayes
[00:29:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:54] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:54] Found gzip - /bin/gzip
[00:29:54] Found vt - /usr/local/bin/vt
[00:29:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:30:39] This is snippy 4.6.0Show full stderr[00:30:39] This is snippy 4.6.0
[00:30:39] Written by Torsten Seemann
[00:30:39] Obtained from https://github.com/tseemann/snippy
[00:30:39] Detected operating system: linux
[00:30:39] Enabling bundled linux tools.
[00:30:39] Found bwa - /usr/local/bin/bwa
[00:30:39] Found bcftools - /usr/local/bin/bcftools
[00:30:39] Found samtools - /usr/local/bin/samtools
[00:30:39] Found java - /usr/local/bin/java
[00:30:39] Found snpEff - /usr/local/bin/snpEff
[00:30:39] Found samclip - /usr/local/bin/samclip
[00:30:39] Found seqtk - /usr/local/bin/seqtk
[00:30:39] Found parallel - /usr/local/bin/parallel
[00:30:39] Found freebayes - /usr/local/bin/freebayes
[00:30:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:30:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:30:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:30:39] Found vcfuniq - /usr/local/bin/vcfuniq
[00:30:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:30:39] Found gzip - /bin/gzip
[00:30:39] Found vt - /usr/local/bin/vt
[00:30:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:30:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:30:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:30:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:30:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:30:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:30:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:30:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:30:42] This is snippy 4.6.0Show full stderr[00:30:42] This is snippy 4.6.0
[00:30:42] Written by Torsten Seemann
[00:30:42] Obtained from https://github.com/tseemann/snippy
[00:30:42] Detected operating system: linux
[00:30:42] Enabling bundled linux tools.
[00:30:42] Found bwa - /usr/local/bin/bwa
[00:30:42] Found bcftools - /usr/local/bin/bcftools
[00:30:42] Found samtools - /usr/local/bin/samtools
[00:30:42] Found java - /usr/local/bin/java
[00:30:42] Found snpEff - /usr/local/bin/snpEff
[00:30:42] Found samclip - /usr/local/bin/samclip
[00:30:42] Found seqtk - /usr/local/bin/seqtk
[00:30:42] Found parallel - /usr/local/bin/parallel
[00:30:42] Found freebayes - /usr/local/bin/freebayes
[00:30:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:30:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:30:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:30:42] Found vcfuniq - /usr/local/bin/vcfuniq
[00:30:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:30:42] Found gzip - /bin/gzip
[00:30:42] Found vt - /usr/local/bin/vt
[00:30:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:30:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:30:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:30:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:30:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:30:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:30:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:30:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:30:44] This is snippy 4.6.0Show full stderr[00:30:44] This is snippy 4.6.0
[00:30:44] Written by Torsten Seemann
[00:30:44] Obtained from https://github.com/tseemann/snippy
[00:30:44] Detected operating system: linux
[00:30:44] Enabling bundled linux tools.
[00:30:44] Found bwa - /usr/local/bin/bwa
[00:30:44] Found bcftools - /usr/local/bin/bcftools
[00:30:44] Found samtools - /usr/local/bin/samtools
[00:30:44] Found java - /usr/local/bin/java
[00:30:44] Found snpEff - /usr/local/bin/snpEff
[00:30:44] Found samclip - /usr/local/bin/samclip
[00:30:44] Found seqtk - /usr/local/bin/seqtk
[00:30:44] Found parallel - /usr/local/bin/parallel
[00:30:44] Found freebayes - /usr/local/bin/freebayes
[00:30:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:30:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:30:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:30:44] Found vcfuniq - /usr/local/bin/vcfuniq
[00:30:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:30:44] Found gzip - /bin/gzip
[00:30:44] Found vt - /usr/local/bin/vt
[00:30:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:30:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:30:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:30:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:30:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:30:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:30:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:30:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:00] This is snippy 4.6.0Show full stderr[00:31:00] This is snippy 4.6.0
[00:31:00] Written by Torsten Seemann
[00:31:00] Obtained from https://github.com/tseemann/snippy
[00:31:00] Detected operating system: linux
[00:31:00] Enabling bundled linux tools.
[00:31:00] Found bwa - /usr/local/bin/bwa
[00:31:00] Found bcftools - /usr/local/bin/bcftools
[00:31:00] Found samtools - /usr/local/bin/samtools
[00:31:00] Found java - /usr/local/bin/java
[00:31:00] Found snpEff - /usr/local/bin/snpEff
[00:31:00] Found samclip - /usr/local/bin/samclip
[00:31:00] Found seqtk - /usr/local/bin/seqtk
[00:31:00] Found parallel - /usr/local/bin/parallel
[00:31:00] Found freebayes - /usr/local/bin/freebayes
[00:31:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:00] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:00] Found gzip - /bin/gzip
[00:31:00] Found vt - /usr/local/bin/vt
[00:31:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:06] This is snippy 4.6.0Show full stderr[00:31:06] This is snippy 4.6.0
[00:31:06] Written by Torsten Seemann
[00:31:06] Obtained from https://github.com/tseemann/snippy
[00:31:06] Detected operating system: linux
[00:31:06] Enabling bundled linux tools.
[00:31:06] Found bwa - /usr/local/bin/bwa
[00:31:06] Found bcftools - /usr/local/bin/bcftools
[00:31:06] Found samtools - /usr/local/bin/samtools
[00:31:06] Found java - /usr/local/bin/java
[00:31:06] Found snpEff - /usr/local/bin/snpEff
[00:31:06] Found samclip - /usr/local/bin/samclip
[00:31:06] Found seqtk - /usr/local/bin/seqtk
[00:31:06] Found parallel - /usr/local/bin/parallel
[00:31:06] Found freebayes - /usr/local/bin/freebayes
[00:31:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:06] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:06] Found gzip - /bin/gzip
[00:31:06] Found vt - /usr/local/bin/vt
[00:31:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:27:51] This is snippy 4.6.0Show full stderr[00:27:51] This is snippy 4.6.0
[00:27:51] Written by Torsten Seemann
[00:27:51] Obtained from https://github.com/tseemann/snippy
[00:27:51] Detected operating system: linux
[00:27:51] Enabling bundled linux tools.
[00:27:51] Found bwa - /usr/local/bin/bwa
[00:27:51] Found bcftools - /usr/local/bin/bcftools
[00:27:51] Found samtools - /usr/local/bin/samtools
[00:27:51] Found java - /usr/local/bin/java
[00:27:51] Found snpEff - /usr/local/bin/snpEff
[00:27:51] Found samclip - /usr/local/bin/samclip
[00:27:51] Found seqtk - /usr/local/bin/seqtk
[00:27:51] Found parallel - /usr/local/bin/parallel
[00:27:51] Found freebayes - /usr/local/bin/freebayes
[00:27:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:27:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:27:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:27:51] Found vcfuniq - /usr/local/bin/vcfuniq
[00:27:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:27:51] Found gzip - /bin/gzip
[00:27:51] Found vt - /usr/local/bin/vt
[00:27:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:27:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:27:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:27:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:27:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:27:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:27:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:27:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:27:54] This is snippy 4.6.0Show full stderr[00:27:54] This is snippy 4.6.0
[00:27:54] Written by Torsten Seemann
[00:27:54] Obtained from https://github.com/tseemann/snippy
[00:27:54] Detected operating system: linux
[00:27:54] Enabling bundled linux tools.
[00:27:54] Found bwa - /usr/local/bin/bwa
[00:27:54] Found bcftools - /usr/local/bin/bcftools
[00:27:54] Found samtools - /usr/local/bin/samtools
[00:27:54] Found java - /usr/local/bin/java
[00:27:54] Found snpEff - /usr/local/bin/snpEff
[00:27:54] Found samclip - /usr/local/bin/samclip
[00:27:55] Found seqtk - /usr/local/bin/seqtk
[00:27:55] Found parallel - /usr/local/bin/parallel
[00:27:55] Found freebayes - /usr/local/bin/freebayes
[00:27:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:27:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:27:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:27:55] Found vcfuniq - /usr/local/bin/vcfuniq
[00:27:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:27:55] Found gzip - /bin/gzip
[00:27:55] Found vt - /usr/local/bin/vt
[00:27:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:27:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:27:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:27:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:27:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:27:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:27:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:27:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:28:39] This is snippy 4.6.0Show full stderr[00:28:39] This is snippy 4.6.0
[00:28:39] Written by Torsten Seemann
[00:28:39] Obtained from https://github.com/tseemann/snippy
[00:28:39] Detected operating system: linux
[00:28:39] Enabling bundled linux tools.
[00:28:39] Found bwa - /usr/local/bin/bwa
[00:28:39] Found bcftools - /usr/local/bin/bcftools
[00:28:39] Found samtools - /usr/local/bin/samtools
[00:28:39] Found java - /usr/local/bin/java
[00:28:39] Found snpEff - /usr/local/bin/snpEff
[00:28:39] Found samclip - /usr/local/bin/samclip
[00:28:39] Found seqtk - /usr/local/bin/seqtk
[00:28:39] Found parallel - /usr/local/bin/parallel
[00:28:39] Found freebayes - /usr/local/bin/freebayes
[00:28:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:28:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:28:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:28:39] Found vcfuniq - /usr/local/bin/vcfuniq
[00:28:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:28:39] Found gzip - /bin/gzip
[00:28:39] Found vt - /usr/local/bin/vt
[00:28:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:28:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:28:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:28:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:28:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:28:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:28:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:28:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:15] This is snippy 4.6.0Show full stderr[00:29:15] This is snippy 4.6.0
[00:29:15] Written by Torsten Seemann
[00:29:15] Obtained from https://github.com/tseemann/snippy
[00:29:15] Detected operating system: linux
[00:29:15] Enabling bundled linux tools.
[00:29:15] Found bwa - /usr/local/bin/bwa
[00:29:15] Found bcftools - /usr/local/bin/bcftools
[00:29:15] Found samtools - /usr/local/bin/samtools
[00:29:15] Found java - /usr/local/bin/java
[00:29:15] Found snpEff - /usr/local/bin/snpEff
[00:29:15] Found samclip - /usr/local/bin/samclip
[00:29:15] Found seqtk - /usr/local/bin/seqtk
[00:29:15] Found parallel - /usr/local/bin/parallel
[00:29:15] Found freebayes - /usr/local/bin/freebayes
[00:29:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:15] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:15] Found gzip - /bin/gzip
[00:29:15] Found vt - /usr/local/bin/vt
[00:29:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:27] This is snippy 4.6.0Show full stderr[00:29:27] This is snippy 4.6.0
[00:29:27] Written by Torsten Seemann
[00:29:27] Obtained from https://github.com/tseemann/snippy
[00:29:27] Detected operating system: linux
[00:29:27] Enabling bundled linux tools.
[00:29:27] Found bwa - /usr/local/bin/bwa
[00:29:27] Found bcftools - /usr/local/bin/bcftools
[00:29:27] Found samtools - /usr/local/bin/samtools
[00:29:27] Found java - /usr/local/bin/java
[00:29:27] Found snpEff - /usr/local/bin/snpEff
[00:29:27] Found samclip - /usr/local/bin/samclip
[00:29:27] Found seqtk - /usr/local/bin/seqtk
[00:29:27] Found parallel - /usr/local/bin/parallel
[00:29:27] Found freebayes - /usr/local/bin/freebayes
[00:29:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:27] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:27] Found gzip - /bin/gzip
[00:29:27] Found vt - /usr/local/bin/vt
[00:29:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:30] This is snippy 4.6.0Show full stderr[00:29:30] This is snippy 4.6.0
[00:29:30] Written by Torsten Seemann
[00:29:30] Obtained from https://github.com/tseemann/snippy
[00:29:30] Detected operating system: linux
[00:29:30] Enabling bundled linux tools.
[00:29:30] Found bwa - /usr/local/bin/bwa
[00:29:30] Found bcftools - /usr/local/bin/bcftools
[00:29:30] Found samtools - /usr/local/bin/samtools
[00:29:30] Found java - /usr/local/bin/java
[00:29:30] Found snpEff - /usr/local/bin/snpEff
[00:29:30] Found samclip - /usr/local/bin/samclip
[00:29:30] Found seqtk - /usr/local/bin/seqtk
[00:29:30] Found parallel - /usr/local/bin/parallel
[00:29:30] Found freebayes - /usr/local/bin/freebayes
[00:29:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:30] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:30] Found gzip - /bin/gzip
[00:29:30] Found vt - /usr/local/bin/vt
[00:29:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:29] This is snippy 4.6.0Show full stderr[00:29:29] This is snippy 4.6.0
[00:29:29] Written by Torsten Seemann
[00:29:29] Obtained from https://github.com/tseemann/snippy
[00:29:29] Detected operating system: linux
[00:29:29] Enabling bundled linux tools.
[00:29:29] Found bwa - /usr/local/bin/bwa
[00:29:29] Found bcftools - /usr/local/bin/bcftools
[00:29:29] Found samtools - /usr/local/bin/samtools
[00:29:29] Found java - /usr/local/bin/java
[00:29:29] Found snpEff - /usr/local/bin/snpEff
[00:29:30] Found samclip - /usr/local/bin/samclip
[00:29:30] Found seqtk - /usr/local/bin/seqtk
[00:29:30] Found parallel - /usr/local/bin/parallel
[00:29:30] Found freebayes - /usr/local/bin/freebayes
[00:29:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:30] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:30] Found gzip - /bin/gzip
[00:29:30] Found vt - /usr/local/bin/vt
[00:29:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:30] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:30:12] This is snippy 4.6.0Show full stderr[00:30:12] This is snippy 4.6.0
[00:30:12] Written by Torsten Seemann
[00:30:12] Obtained from https://github.com/tseemann/snippy
[00:30:12] Detected operating system: linux
[00:30:12] Enabling bundled linux tools.
[00:30:12] Found bwa - /usr/local/bin/bwa
[00:30:12] Found bcftools - /usr/local/bin/bcftools
[00:30:12] Found samtools - /usr/local/bin/samtools
[00:30:12] Found java - /usr/local/bin/java
[00:30:12] Found snpEff - /usr/local/bin/snpEff
[00:30:12] Found samclip - /usr/local/bin/samclip
[00:30:12] Found seqtk - /usr/local/bin/seqtk
[00:30:12] Found parallel - /usr/local/bin/parallel
[00:30:12] Found freebayes - /usr/local/bin/freebayes
[00:30:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:30:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:30:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:30:12] Found vcfuniq - /usr/local/bin/vcfuniq
[00:30:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:30:12] Found gzip - /bin/gzip
[00:30:12] Found vt - /usr/local/bin/vt
[00:30:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:30:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:30:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:30:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:30:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:30:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:30:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:30:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:30:24] This is snippy 4.6.0Show full stderr[00:30:24] This is snippy 4.6.0
[00:30:24] Written by Torsten Seemann
[00:30:24] Obtained from https://github.com/tseemann/snippy
[00:30:24] Detected operating system: linux
[00:30:24] Enabling bundled linux tools.
[00:30:24] Found bwa - /usr/local/bin/bwa
[00:30:24] Found bcftools - /usr/local/bin/bcftools
[00:30:24] Found samtools - /usr/local/bin/samtools
[00:30:24] Found java - /usr/local/bin/java
[00:30:24] Found snpEff - /usr/local/bin/snpEff
[00:30:24] Found samclip - /usr/local/bin/samclip
[00:30:24] Found seqtk - /usr/local/bin/seqtk
[00:30:24] Found parallel - /usr/local/bin/parallel
[00:30:24] Found freebayes - /usr/local/bin/freebayes
[00:30:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:30:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:30:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:30:24] Found vcfuniq - /usr/local/bin/vcfuniq
[00:30:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:30:24] Found gzip - /bin/gzip
[00:30:24] Found vt - /usr/local/bin/vt
[00:30:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:30:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:30:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:30:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:30:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:30:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:30:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:30:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:44] This is snippy 4.6.0Show full stderr[00:31:44] This is snippy 4.6.0
[00:31:44] Written by Torsten Seemann
[00:31:44] Obtained from https://github.com/tseemann/snippy
[00:31:44] Detected operating system: linux
[00:31:44] Enabling bundled linux tools.
[00:31:44] Found bwa - /usr/local/bin/bwa
[00:31:44] Found bcftools - /usr/local/bin/bcftools
[00:31:44] Found samtools - /usr/local/bin/samtools
[00:31:44] Found java - /usr/local/bin/java
[00:31:44] Found snpEff - /usr/local/bin/snpEff
[00:31:44] Found samclip - /usr/local/bin/samclip
[00:31:44] Found seqtk - /usr/local/bin/seqtk
[00:31:44] Found parallel - /usr/local/bin/parallel
[00:31:44] Found freebayes - /usr/local/bin/freebayes
[00:31:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:44] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:44] Found gzip - /bin/gzip
[00:31:44] Found vt - /usr/local/bin/vt
[00:31:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:51] This is snippy 4.6.0Show full stderr[00:31:51] This is snippy 4.6.0
[00:31:51] Written by Torsten Seemann
[00:31:51] Obtained from https://github.com/tseemann/snippy
[00:31:51] Detected operating system: linux
[00:31:51] Enabling bundled linux tools.
[00:31:51] Found bwa - /usr/local/bin/bwa
[00:31:51] Found bcftools - /usr/local/bin/bcftools
[00:31:51] Found samtools - /usr/local/bin/samtools
[00:31:51] Found java - /usr/local/bin/java
[00:31:51] Found snpEff - /usr/local/bin/snpEff
[00:31:51] Found samclip - /usr/local/bin/samclip
[00:31:51] Found seqtk - /usr/local/bin/seqtk
[00:31:51] Found parallel - /usr/local/bin/parallel
[00:31:51] Found freebayes - /usr/local/bin/freebayes
[00:31:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:51] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:51] Found gzip - /bin/gzip
[00:31:51] Found vt - /usr/local/bin/vt
[00:31:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:32:31] This is snippy 4.6.0Show full stderr[00:32:31] This is snippy 4.6.0
[00:32:31] Written by Torsten Seemann
[00:32:31] Obtained from https://github.com/tseemann/snippy
[00:32:31] Detected operating system: linux
[00:32:31] Enabling bundled linux tools.
[00:32:31] Found bwa - /usr/local/bin/bwa
[00:32:31] Found bcftools - /usr/local/bin/bcftools
[00:32:31] Found samtools - /usr/local/bin/samtools
[00:32:31] Found java - /usr/local/bin/java
[00:32:31] Found snpEff - /usr/local/bin/snpEff
[00:32:31] Found samclip - /usr/local/bin/samclip
[00:32:31] Found seqtk - /usr/local/bin/seqtk
[00:32:31] Found parallel - /usr/local/bin/parallel
[00:32:31] Found freebayes - /usr/local/bin/freebayes
[00:32:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:32:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:32:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:32:31] Found vcfuniq - /usr/local/bin/vcfuniq
[00:32:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:32:31] Found gzip - /bin/gzip
[00:32:31] Found vt - /usr/local/bin/vt
[00:32:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:32:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:32:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:32:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:32:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:32:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:32:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:32:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:33:12] This is snippy 4.6.0Show full stderr[00:33:12] This is snippy 4.6.0
[00:33:12] Written by Torsten Seemann
[00:33:12] Obtained from https://github.com/tseemann/snippy
[00:33:12] Detected operating system: linux
[00:33:12] Enabling bundled linux tools.
[00:33:12] Found bwa - /usr/local/bin/bwa
[00:33:12] Found bcftools - /usr/local/bin/bcftools
[00:33:12] Found samtools - /usr/local/bin/samtools
[00:33:12] Found java - /usr/local/bin/java
[00:33:12] Found snpEff - /usr/local/bin/snpEff
[00:33:12] Found samclip - /usr/local/bin/samclip
[00:33:12] Found seqtk - /usr/local/bin/seqtk
[00:33:12] Found parallel - /usr/local/bin/parallel
[00:33:12] Found freebayes - /usr/local/bin/freebayes
[00:33:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:12] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:12] Found gzip - /bin/gzip
[00:33:12] Found vt - /usr/local/bin/vt
[00:33:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:59:04] This is snippy 4.6.0Show full stderr[00:59:04] This is snippy 4.6.0
[00:59:04] Written by Torsten Seemann
[00:59:04] Obtained from https://github.com/tseemann/snippy
[00:59:04] Detected operating system: linux
[00:59:04] Enabling bundled linux tools.
[00:59:04] Found bwa - /usr/local/bin/bwa
[00:59:04] Found bcftools - /usr/local/bin/bcftools
[00:59:04] Found samtools - /usr/local/bin/samtools
[00:59:04] Found java - /usr/local/bin/java
[00:59:04] Found snpEff - /usr/local/bin/snpEff
[00:59:04] Found samclip - /usr/local/bin/samclip
[00:59:04] Found seqtk - /usr/local/bin/seqtk
[00:59:04] Found parallel - /usr/local/bin/parallel
[00:59:04] Found freebayes - /usr/local/bin/freebayes
[00:59:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:59:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:59:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:59:04] Found vcfuniq - /usr/local/bin/vcfuniq
[00:59:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:59:04] Found gzip - /bin/gzip
[00:59:04] Found vt - /usr/local/bin/vt
[00:59:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:59:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:59:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:59:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:59:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:59:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:59:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:59:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:04:33] This is snippy 4.6.0Show full stderr[01:04:33] This is snippy 4.6.0
[01:04:33] Written by Torsten Seemann
[01:04:33] Obtained from https://github.com/tseemann/snippy
[01:04:33] Detected operating system: linux
[01:04:33] Enabling bundled linux tools.
[01:04:33] Found bwa - /usr/local/bin/bwa
[01:04:33] Found bcftools - /usr/local/bin/bcftools
[01:04:33] Found samtools - /usr/local/bin/samtools
[01:04:33] Found java - /usr/local/bin/java
[01:04:33] Found snpEff - /usr/local/bin/snpEff
[01:04:33] Found samclip - /usr/local/bin/samclip
[01:04:33] Found seqtk - /usr/local/bin/seqtk
[01:04:33] Found parallel - /usr/local/bin/parallel
[01:04:33] Found freebayes - /usr/local/bin/freebayes
[01:04:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:04:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:04:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:04:33] Found vcfuniq - /usr/local/bin/vcfuniq
[01:04:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:04:33] Found gzip - /bin/gzip
[01:04:33] Found vt - /usr/local/bin/vt
[01:04:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:04:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:04:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:04:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:04:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:04:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:04:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:04:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:04:51] This is snippy 4.6.0Show full stderr[01:04:51] This is snippy 4.6.0
[01:04:51] Written by Torsten Seemann
[01:04:51] Obtained from https://github.com/tseemann/snippy
[01:04:51] Detected operating system: linux
[01:04:51] Enabling bundled linux tools.
[01:04:51] Found bwa - /usr/local/bin/bwa
[01:04:51] Found bcftools - /usr/local/bin/bcftools
[01:04:51] Found samtools - /usr/local/bin/samtools
[01:04:51] Found java - /usr/local/bin/java
[01:04:51] Found snpEff - /usr/local/bin/snpEff
[01:04:51] Found samclip - /usr/local/bin/samclip
[01:04:51] Found seqtk - /usr/local/bin/seqtk
[01:04:51] Found parallel - /usr/local/bin/parallel
[01:04:51] Found freebayes - /usr/local/bin/freebayes
[01:04:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:04:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:04:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:04:51] Found vcfuniq - /usr/local/bin/vcfuniq
[01:04:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:04:52] Found gzip - /bin/gzip
[01:04:52] Found vt - /usr/local/bin/vt
[01:04:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:04:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:04:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:04:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:04:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:04:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:04:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:04:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:05:30] This is snippy 4.6.0Show full stderr[01:05:30] This is snippy 4.6.0
[01:05:30] Written by Torsten Seemann
[01:05:30] Obtained from https://github.com/tseemann/snippy
[01:05:30] Detected operating system: linux
[01:05:30] Enabling bundled linux tools.
[01:05:30] Found bwa - /usr/local/bin/bwa
[01:05:31] Found bcftools - /usr/local/bin/bcftools
[01:05:31] Found samtools - /usr/local/bin/samtools
[01:05:31] Found java - /usr/local/bin/java
[01:05:31] Found snpEff - /usr/local/bin/snpEff
[01:05:31] Found samclip - /usr/local/bin/samclip
[01:05:31] Found seqtk - /usr/local/bin/seqtk
[01:05:31] Found parallel - /usr/local/bin/parallel
[01:05:31] Found freebayes - /usr/local/bin/freebayes
[01:05:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:05:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:05:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:05:31] Found vcfuniq - /usr/local/bin/vcfuniq
[01:05:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:05:31] Found gzip - /bin/gzip
[01:05:31] Found vt - /usr/local/bin/vt
[01:05:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:05:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:05:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:05:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:05:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:05:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:05:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:05:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:07:19] This is snippy 4.6.0Show full stderr[01:07:19] This is snippy 4.6.0
[01:07:19] Written by Torsten Seemann
[01:07:19] Obtained from https://github.com/tseemann/snippy
[01:07:19] Detected operating system: linux
[01:07:19] Enabling bundled linux tools.
[01:07:19] Found bwa - /usr/local/bin/bwa
[01:07:19] Found bcftools - /usr/local/bin/bcftools
[01:07:19] Found samtools - /usr/local/bin/samtools
[01:07:19] Found java - /usr/local/bin/java
[01:07:19] Found snpEff - /usr/local/bin/snpEff
[01:07:19] Found samclip - /usr/local/bin/samclip
[01:07:19] Found seqtk - /usr/local/bin/seqtk
[01:07:19] Found parallel - /usr/local/bin/parallel
[01:07:19] Found freebayes - /usr/local/bin/freebayes
[01:07:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:07:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:07:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:07:19] Found vcfuniq - /usr/local/bin/vcfuniq
[01:07:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:07:19] Found gzip - /bin/gzip
[01:07:19] Found vt - /usr/local/bin/vt
[01:07:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:07:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:07:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:07:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:07:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:07:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:07:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:07:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:13:42] This is snippy 4.6.0Show full stderr[01:13:42] This is snippy 4.6.0
[01:13:42] Written by Torsten Seemann
[01:13:42] Obtained from https://github.com/tseemann/snippy
[01:13:42] Detected operating system: linux
[01:13:42] Enabling bundled linux tools.
[01:13:42] Found bwa - /usr/local/bin/bwa
[01:13:42] Found bcftools - /usr/local/bin/bcftools
[01:13:42] Found samtools - /usr/local/bin/samtools
[01:13:42] Found java - /usr/local/bin/java
[01:13:42] Found snpEff - /usr/local/bin/snpEff
[01:13:42] Found samclip - /usr/local/bin/samclip
[01:13:42] Found seqtk - /usr/local/bin/seqtk
[01:13:42] Found parallel - /usr/local/bin/parallel
[01:13:42] Found freebayes - /usr/local/bin/freebayes
[01:13:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:13:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:13:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:13:42] Found vcfuniq - /usr/local/bin/vcfuniq
[01:13:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:13:42] Found gzip - /bin/gzip
[01:13:42] Found vt - /usr/local/bin/vt
[01:13:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:13:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:13:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:13:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:13:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:13:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:13:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:13:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:14:06] This is snippy 4.6.0Show full stderr[01:14:06] This is snippy 4.6.0
[01:14:06] Written by Torsten Seemann
[01:14:06] Obtained from https://github.com/tseemann/snippy
[01:14:06] Detected operating system: linux
[01:14:06] Enabling bundled linux tools.
[01:14:06] Found bwa - /usr/local/bin/bwa
[01:14:06] Found bcftools - /usr/local/bin/bcftools
[01:14:06] Found samtools - /usr/local/bin/samtools
[01:14:06] Found java - /usr/local/bin/java
[01:14:06] Found snpEff - /usr/local/bin/snpEff
[01:14:06] Found samclip - /usr/local/bin/samclip
[01:14:06] Found seqtk - /usr/local/bin/seqtk
[01:14:06] Found parallel - /usr/local/bin/parallel
[01:14:06] Found freebayes - /usr/local/bin/freebayes
[01:14:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:14:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:14:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:14:06] Found vcfuniq - /usr/local/bin/vcfuniq
[01:14:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:14:06] Found gzip - /bin/gzip
[01:14:06] Found vt - /usr/local/bin/vt
[01:14:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:14:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:14:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:14:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:14:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:14:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:14:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:14:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:15:39] This is snippy 4.6.0Show full stderr[01:15:39] This is snippy 4.6.0
[01:15:39] Written by Torsten Seemann
[01:15:39] Obtained from https://github.com/tseemann/snippy
[01:15:39] Detected operating system: linux
[01:15:39] Enabling bundled linux tools.
[01:15:39] Found bwa - /usr/local/bin/bwa
[01:15:39] Found bcftools - /usr/local/bin/bcftools
[01:15:39] Found samtools - /usr/local/bin/samtools
[01:15:39] Found java - /usr/local/bin/java
[01:15:39] Found snpEff - /usr/local/bin/snpEff
[01:15:39] Found samclip - /usr/local/bin/samclip
[01:15:39] Found seqtk - /usr/local/bin/seqtk
[01:15:39] Found parallel - /usr/local/bin/parallel
[01:15:39] Found freebayes - /usr/local/bin/freebayes
[01:15:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:15:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:15:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:15:39] Found vcfuniq - /usr/local/bin/vcfuniq
[01:15:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:15:39] Found gzip - /bin/gzip
[01:15:39] Found vt - /usr/local/bin/vt
[01:15:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:15:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:15:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:15:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:15:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:15:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:15:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:15:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:20:52] This is snippy 4.6.0Show full stderr[01:20:52] This is snippy 4.6.0
[01:20:52] Written by Torsten Seemann
[01:20:52] Obtained from https://github.com/tseemann/snippy
[01:20:52] Detected operating system: linux
[01:20:52] Enabling bundled linux tools.
[01:20:52] Found bwa - /usr/local/bin/bwa
[01:20:53] Found bcftools - /usr/local/bin/bcftools
[01:20:53] Found samtools - /usr/local/bin/samtools
[01:20:53] Found java - /usr/local/bin/java
[01:20:53] Found snpEff - /usr/local/bin/snpEff
[01:20:53] Found samclip - /usr/local/bin/samclip
[01:20:53] Found seqtk - /usr/local/bin/seqtk
[01:20:53] Found parallel - /usr/local/bin/parallel
[01:20:53] Found freebayes - /usr/local/bin/freebayes
[01:20:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:20:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:20:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:20:53] Found vcfuniq - /usr/local/bin/vcfuniq
[01:20:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:20:53] Found gzip - /bin/gzip
[01:20:53] Found vt - /usr/local/bin/vt
[01:20:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:20:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:20:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:20:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:20:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:20:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:20:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:20:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:24:37] This is snippy 4.6.0Show full stderr[01:24:37] This is snippy 4.6.0
[01:24:37] Written by Torsten Seemann
[01:24:37] Obtained from https://github.com/tseemann/snippy
[01:24:37] Detected operating system: linux
[01:24:37] Enabling bundled linux tools.
[01:24:37] Found bwa - /usr/local/bin/bwa
[01:24:37] Found bcftools - /usr/local/bin/bcftools
[01:24:37] Found samtools - /usr/local/bin/samtools
[01:24:37] Found java - /usr/local/bin/java
[01:24:37] Found snpEff - /usr/local/bin/snpEff
[01:24:37] Found samclip - /usr/local/bin/samclip
[01:24:37] Found seqtk - /usr/local/bin/seqtk
[01:24:37] Found parallel - /usr/local/bin/parallel
[01:24:37] Found freebayes - /usr/local/bin/freebayes
[01:24:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:24:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:24:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:24:37] Found vcfuniq - /usr/local/bin/vcfuniq
[01:24:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:24:37] Found gzip - /bin/gzip
[01:24:37] Found vt - /usr/local/bin/vt
[01:24:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:24:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:24:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:24:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:24:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:24:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:24:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:24:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:30:37] This is snippy 4.6.0Show full stderr[01:30:37] This is snippy 4.6.0
[01:30:37] Written by Torsten Seemann
[01:30:37] Obtained from https://github.com/tseemann/snippy
[01:30:37] Detected operating system: linux
[01:30:37] Enabling bundled linux tools.
[01:30:37] Found bwa - /usr/local/bin/bwa
[01:30:37] Found bcftools - /usr/local/bin/bcftools
[01:30:37] Found samtools - /usr/local/bin/samtools
[01:30:37] Found java - /usr/local/bin/java
[01:30:37] Found snpEff - /usr/local/bin/snpEff
[01:30:37] Found samclip - /usr/local/bin/samclip
[01:30:37] Found seqtk - /usr/local/bin/seqtk
[01:30:37] Found parallel - /usr/local/bin/parallel
[01:30:37] Found freebayes - /usr/local/bin/freebayes
[01:30:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:30:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:30:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:30:37] Found vcfuniq - /usr/local/bin/vcfuniq
[01:30:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:30:37] Found gzip - /bin/gzip
[01:30:37] Found vt - /usr/local/bin/vt
[01:30:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:30:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:30:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:30:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:30:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:30:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:30:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:30:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:21:42] This is snippy 4.6.0Show full stderr[01:21:42] This is snippy 4.6.0
[01:21:42] Written by Torsten Seemann
[01:21:42] Obtained from https://github.com/tseemann/snippy
[01:21:42] Detected operating system: linux
[01:21:42] Enabling bundled linux tools.
[01:21:42] Found bwa - /usr/local/bin/bwa
[01:21:42] Found bcftools - /usr/local/bin/bcftools
[01:21:42] Found samtools - /usr/local/bin/samtools
[01:21:42] Found java - /usr/local/bin/java
[01:21:42] Found snpEff - /usr/local/bin/snpEff
[01:21:42] Found samclip - /usr/local/bin/samclip
[01:21:42] Found seqtk - /usr/local/bin/seqtk
[01:21:42] Found parallel - /usr/local/bin/parallel
[01:21:42] Found freebayes - /usr/local/bin/freebayes
[01:21:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:21:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:21:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:21:42] Found vcfuniq - /usr/local/bin/vcfuniq
[01:21:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:21:42] Found gzip - /bin/gzip
[01:21:42] Found vt - /usr/local/bin/vt
[01:21:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:21:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:21:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:21:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:21:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:21:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:21:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:21:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:22:22] This is snippy 4.6.0Show full stderr[01:22:22] This is snippy 4.6.0
[01:22:22] Written by Torsten Seemann
[01:22:22] Obtained from https://github.com/tseemann/snippy
[01:22:22] Detected operating system: linux
[01:22:22] Enabling bundled linux tools.
[01:22:22] Found bwa - /usr/local/bin/bwa
[01:22:22] Found bcftools - /usr/local/bin/bcftools
[01:22:22] Found samtools - /usr/local/bin/samtools
[01:22:22] Found java - /usr/local/bin/java
[01:22:22] Found snpEff - /usr/local/bin/snpEff
[01:22:22] Found samclip - /usr/local/bin/samclip
[01:22:22] Found seqtk - /usr/local/bin/seqtk
[01:22:22] Found parallel - /usr/local/bin/parallel
[01:22:22] Found freebayes - /usr/local/bin/freebayes
[01:22:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:22:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:22:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:22:22] Found vcfuniq - /usr/local/bin/vcfuniq
[01:22:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:22:22] Found gzip - /bin/gzip
[01:22:22] Found vt - /usr/local/bin/vt
[01:22:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:22:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:22:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:22:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:22:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:22:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:22:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:22:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:22:39] This is snippy 4.6.0Show full stderr[01:22:39] This is snippy 4.6.0
[01:22:39] Written by Torsten Seemann
[01:22:39] Obtained from https://github.com/tseemann/snippy
[01:22:39] Detected operating system: linux
[01:22:39] Enabling bundled linux tools.
[01:22:39] Found bwa - /usr/local/bin/bwa
[01:22:39] Found bcftools - /usr/local/bin/bcftools
[01:22:39] Found samtools - /usr/local/bin/samtools
[01:22:39] Found java - /usr/local/bin/java
[01:22:39] Found snpEff - /usr/local/bin/snpEff
[01:22:39] Found samclip - /usr/local/bin/samclip
[01:22:39] Found seqtk - /usr/local/bin/seqtk
[01:22:39] Found parallel - /usr/local/bin/parallel
[01:22:39] Found freebayes - /usr/local/bin/freebayes
[01:22:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:22:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:22:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:22:39] Found vcfuniq - /usr/local/bin/vcfuniq
[01:22:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:22:39] Found gzip - /bin/gzip
[01:22:39] Found vt - /usr/local/bin/vt
[01:22:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:22:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:22:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:22:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:22:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:22:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:22:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:22:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:22:54] This is snippy 4.6.0Show full stderr[01:22:54] This is snippy 4.6.0
[01:22:54] Written by Torsten Seemann
[01:22:54] Obtained from https://github.com/tseemann/snippy
[01:22:54] Detected operating system: linux
[01:22:54] Enabling bundled linux tools.
[01:22:54] Found bwa - /usr/local/bin/bwa
[01:22:54] Found bcftools - /usr/local/bin/bcftools
[01:22:54] Found samtools - /usr/local/bin/samtools
[01:22:54] Found java - /usr/local/bin/java
[01:22:54] Found snpEff - /usr/local/bin/snpEff
[01:22:54] Found samclip - /usr/local/bin/samclip
[01:22:54] Found seqtk - /usr/local/bin/seqtk
[01:22:54] Found parallel - /usr/local/bin/parallel
[01:22:54] Found freebayes - /usr/local/bin/freebayes
[01:22:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:22:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:22:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:22:54] Found vcfuniq - /usr/local/bin/vcfuniq
[01:22:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:22:54] Found gzip - /bin/gzip
[01:22:54] Found vt - /usr/local/bin/vt
[01:22:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:22:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:22:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:22:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:22:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:22:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:22:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:22:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:29:09] This is snippy 4.6.0Show full stderr[00:29:09] This is snippy 4.6.0
[00:29:09] Written by Torsten Seemann
[00:29:09] Obtained from https://github.com/tseemann/snippy
[00:29:09] Detected operating system: linux
[00:29:09] Enabling bundled linux tools.
[00:29:09] Found bwa - /usr/local/bin/bwa
[00:29:09] Found bcftools - /usr/local/bin/bcftools
[00:29:09] Found samtools - /usr/local/bin/samtools
[00:29:09] Found java - /usr/local/bin/java
[00:29:09] Found snpEff - /usr/local/bin/snpEff
[00:29:09] Found samclip - /usr/local/bin/samclip
[00:29:09] Found seqtk - /usr/local/bin/seqtk
[00:29:09] Found parallel - /usr/local/bin/parallel
[00:29:09] Found freebayes - /usr/local/bin/freebayes
[00:29:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:29:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:29:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:29:09] Found vcfuniq - /usr/local/bin/vcfuniq
[00:29:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:29:09] Found gzip - /bin/gzip
[00:29:09] Found vt - /usr/local/bin/vt
[00:29:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:29:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:29:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:29:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:29:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:29:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:29:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:29:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:32:45] This is snippy 4.6.0Show full stderr[00:32:45] This is snippy 4.6.0
[00:32:45] Written by Torsten Seemann
[00:32:45] Obtained from https://github.com/tseemann/snippy
[00:32:45] Detected operating system: linux
[00:32:45] Enabling bundled linux tools.
[00:32:45] Found bwa - /usr/local/bin/bwa
[00:32:45] Found bcftools - /usr/local/bin/bcftools
[00:32:45] Found samtools - /usr/local/bin/samtools
[00:32:45] Found java - /usr/local/bin/java
[00:32:45] Found snpEff - /usr/local/bin/snpEff
[00:32:45] Found samclip - /usr/local/bin/samclip
[00:32:45] Found seqtk - /usr/local/bin/seqtk
[00:32:45] Found parallel - /usr/local/bin/parallel
[00:32:45] Found freebayes - /usr/local/bin/freebayes
[00:32:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:32:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:32:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:32:45] Found vcfuniq - /usr/local/bin/vcfuniq
[00:32:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:32:45] Found gzip - /bin/gzip
[00:32:45] Found vt - /usr/local/bin/vt
[00:32:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:32:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:32:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:32:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:32:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:32:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:32:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:32:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:33:09] This is snippy 4.6.0Show full stderr[00:33:09] This is snippy 4.6.0
[00:33:09] Written by Torsten Seemann
[00:33:09] Obtained from https://github.com/tseemann/snippy
[00:33:09] Detected operating system: linux
[00:33:09] Enabling bundled linux tools.
[00:33:09] Found bwa - /usr/local/bin/bwa
[00:33:09] Found bcftools - /usr/local/bin/bcftools
[00:33:09] Found samtools - /usr/local/bin/samtools
[00:33:09] Found java - /usr/local/bin/java
[00:33:09] Found snpEff - /usr/local/bin/snpEff
[00:33:09] Found samclip - /usr/local/bin/samclip
[00:33:09] Found seqtk - /usr/local/bin/seqtk
[00:33:09] Found parallel - /usr/local/bin/parallel
[00:33:09] Found freebayes - /usr/local/bin/freebayes
[00:33:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:09] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:09] Found gzip - /bin/gzip
[00:33:09] Found vt - /usr/local/bin/vt
[00:33:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:33:44] This is snippy 4.6.0Show full stderr[00:33:44] This is snippy 4.6.0
[00:33:44] Written by Torsten Seemann
[00:33:44] Obtained from https://github.com/tseemann/snippy
[00:33:44] Detected operating system: linux
[00:33:44] Enabling bundled linux tools.
[00:33:44] Found bwa - /usr/local/bin/bwa
[00:33:44] Found bcftools - /usr/local/bin/bcftools
[00:33:44] Found samtools - /usr/local/bin/samtools
[00:33:44] Found java - /usr/local/bin/java
[00:33:44] Found snpEff - /usr/local/bin/snpEff
[00:33:44] Found samclip - /usr/local/bin/samclip
[00:33:44] Found seqtk - /usr/local/bin/seqtk
[00:33:44] Found parallel - /usr/local/bin/parallel
[00:33:44] Found freebayes - /usr/local/bin/freebayes
[00:33:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:44] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:44] Found gzip - /bin/gzip
[00:33:44] Found vt - /usr/local/bin/vt
[00:33:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:34:24] This is snippy 4.6.0Show full stderr[00:34:24] This is snippy 4.6.0
[00:34:24] Written by Torsten Seemann
[00:34:24] Obtained from https://github.com/tseemann/snippy
[00:34:24] Detected operating system: linux
[00:34:24] Enabling bundled linux tools.
[00:34:24] Found bwa - /usr/local/bin/bwa
[00:34:24] Found bcftools - /usr/local/bin/bcftools
[00:34:24] Found samtools - /usr/local/bin/samtools
[00:34:24] Found java - /usr/local/bin/java
[00:34:24] Found snpEff - /usr/local/bin/snpEff
[00:34:24] Found samclip - /usr/local/bin/samclip
[00:34:24] Found seqtk - /usr/local/bin/seqtk
[00:34:24] Found parallel - /usr/local/bin/parallel
[00:34:24] Found freebayes - /usr/local/bin/freebayes
[00:34:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:34:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:34:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:34:24] Found vcfuniq - /usr/local/bin/vcfuniq
[00:34:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:34:24] Found gzip - /bin/gzip
[00:34:24] Found vt - /usr/local/bin/vt
[00:34:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:34:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:34:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:34:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:34:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:34:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:34:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:34:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:34:27] This is snippy 4.6.0Show full stderr[00:34:27] This is snippy 4.6.0
[00:34:27] Written by Torsten Seemann
[00:34:27] Obtained from https://github.com/tseemann/snippy
[00:34:27] Detected operating system: linux
[00:34:27] Enabling bundled linux tools.
[00:34:27] Found bwa - /usr/local/bin/bwa
[00:34:27] Found bcftools - /usr/local/bin/bcftools
[00:34:27] Found samtools - /usr/local/bin/samtools
[00:34:27] Found java - /usr/local/bin/java
[00:34:27] Found snpEff - /usr/local/bin/snpEff
[00:34:27] Found samclip - /usr/local/bin/samclip
[00:34:27] Found seqtk - /usr/local/bin/seqtk
[00:34:27] Found parallel - /usr/local/bin/parallel
[00:34:27] Found freebayes - /usr/local/bin/freebayes
[00:34:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:34:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:34:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:34:27] Found vcfuniq - /usr/local/bin/vcfuniq
[00:34:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:34:27] Found gzip - /bin/gzip
[00:34:27] Found vt - /usr/local/bin/vt
[00:34:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:34:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:34:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:34:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:34:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:34:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:34:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:34:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:34:33] This is snippy 4.6.0Show full stderr[00:34:33] This is snippy 4.6.0
[00:34:33] Written by Torsten Seemann
[00:34:33] Obtained from https://github.com/tseemann/snippy
[00:34:33] Detected operating system: linux
[00:34:33] Enabling bundled linux tools.
[00:34:33] Found bwa - /usr/local/bin/bwa
[00:34:33] Found bcftools - /usr/local/bin/bcftools
[00:34:33] Found samtools - /usr/local/bin/samtools
[00:34:33] Found java - /usr/local/bin/java
[00:34:33] Found snpEff - /usr/local/bin/snpEff
[00:34:33] Found samclip - /usr/local/bin/samclip
[00:34:33] Found seqtk - /usr/local/bin/seqtk
[00:34:33] Found parallel - /usr/local/bin/parallel
[00:34:33] Found freebayes - /usr/local/bin/freebayes
[00:34:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:34:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:34:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:34:33] Found vcfuniq - /usr/local/bin/vcfuniq
[00:34:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:34:33] Found gzip - /bin/gzip
[00:34:33] Found vt - /usr/local/bin/vt
[00:34:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:34:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:34:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:34:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:34:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:34:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:34:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:34:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:35:09] This is snippy 4.6.0Show full stderr[00:35:09] This is snippy 4.6.0
[00:35:09] Written by Torsten Seemann
[00:35:09] Obtained from https://github.com/tseemann/snippy
[00:35:09] Detected operating system: linux
[00:35:09] Enabling bundled linux tools.
[00:35:09] Found bwa - /usr/local/bin/bwa
[00:35:09] Found bcftools - /usr/local/bin/bcftools
[00:35:09] Found samtools - /usr/local/bin/samtools
[00:35:09] Found java - /usr/local/bin/java
[00:35:09] Found snpEff - /usr/local/bin/snpEff
[00:35:09] Found samclip - /usr/local/bin/samclip
[00:35:09] Found seqtk - /usr/local/bin/seqtk
[00:35:09] Found parallel - /usr/local/bin/parallel
[00:35:09] Found freebayes - /usr/local/bin/freebayes
[00:35:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:35:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:35:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:35:10] Found vcfuniq - /usr/local/bin/vcfuniq
[00:35:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:35:10] Found gzip - /bin/gzip
[00:35:10] Found vt - /usr/local/bin/vt
[00:35:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:35:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:35:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:35:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:35:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:35:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:35:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:35:11] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:38:57] This is snippy 4.6.0Show full stderr[00:38:57] This is snippy 4.6.0
[00:38:57] Written by Torsten Seemann
[00:38:57] Obtained from https://github.com/tseemann/snippy
[00:38:57] Detected operating system: linux
[00:38:57] Enabling bundled linux tools.
[00:38:57] Found bwa - /usr/local/bin/bwa
[00:38:57] Found bcftools - /usr/local/bin/bcftools
[00:38:57] Found samtools - /usr/local/bin/samtools
[00:38:57] Found java - /usr/local/bin/java
[00:38:57] Found snpEff - /usr/local/bin/snpEff
[00:38:57] Found samclip - /usr/local/bin/samclip
[00:38:57] Found seqtk - /usr/local/bin/seqtk
[00:38:57] Found parallel - /usr/local/bin/parallel
[00:38:57] Found freebayes - /usr/local/bin/freebayes
[00:38:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:38:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:38:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:38:57] Found vcfuniq - /usr/local/bin/vcfuniq
[00:38:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:38:57] Found gzip - /bin/gzip
[00:38:57] Found vt - /usr/local/bin/vt
[00:38:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:38:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:38:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:38:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:38:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:38:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:38:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:38:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:43:46] This is snippy 4.6.0Show full stderr[00:43:46] This is snippy 4.6.0
[00:43:46] Written by Torsten Seemann
[00:43:46] Obtained from https://github.com/tseemann/snippy
[00:43:46] Detected operating system: linux
[00:43:46] Enabling bundled linux tools.
[00:43:46] Found bwa - /usr/local/bin/bwa
[00:43:46] Found bcftools - /usr/local/bin/bcftools
[00:43:46] Found samtools - /usr/local/bin/samtools
[00:43:46] Found java - /usr/local/bin/java
[00:43:47] Found snpEff - /usr/local/bin/snpEff
[00:43:47] Found samclip - /usr/local/bin/samclip
[00:43:47] Found seqtk - /usr/local/bin/seqtk
[00:43:47] Found parallel - /usr/local/bin/parallel
[00:43:47] Found freebayes - /usr/local/bin/freebayes
[00:43:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:43:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:43:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:43:47] Found vcfuniq - /usr/local/bin/vcfuniq
[00:43:47] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:43:47] Found gzip - /bin/gzip
[00:43:47] Found vt - /usr/local/bin/vt
[00:43:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:43:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:43:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:43:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:43:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:43:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:43:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:43:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:46:49] This is snippy 4.6.0Show full stderr[00:46:49] This is snippy 4.6.0
[00:46:49] Written by Torsten Seemann
[00:46:49] Obtained from https://github.com/tseemann/snippy
[00:46:49] Detected operating system: linux
[00:46:49] Enabling bundled linux tools.
[00:46:49] Found bwa - /usr/local/bin/bwa
[00:46:49] Found bcftools - /usr/local/bin/bcftools
[00:46:49] Found samtools - /usr/local/bin/samtools
[00:46:49] Found java - /usr/local/bin/java
[00:46:49] Found snpEff - /usr/local/bin/snpEff
[00:46:49] Found samclip - /usr/local/bin/samclip
[00:46:49] Found seqtk - /usr/local/bin/seqtk
[00:46:49] Found parallel - /usr/local/bin/parallel
[00:46:49] Found freebayes - /usr/local/bin/freebayes
[00:46:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:46:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:46:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:46:49] Found vcfuniq - /usr/local/bin/vcfuniq
[00:46:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:46:49] Found gzip - /bin/gzip
[00:46:49] Found vt - /usr/local/bin/vt
[00:46:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:46:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:46:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:46:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:46:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:46:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:46:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:46:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:47:04] This is snippy 4.6.0Show full stderr[00:47:04] This is snippy 4.6.0
[00:47:04] Written by Torsten Seemann
[00:47:04] Obtained from https://github.com/tseemann/snippy
[00:47:04] Detected operating system: linux
[00:47:04] Enabling bundled linux tools.
[00:47:04] Found bwa - /usr/local/bin/bwa
[00:47:04] Found bcftools - /usr/local/bin/bcftools
[00:47:04] Found samtools - /usr/local/bin/samtools
[00:47:04] Found java - /usr/local/bin/java
[00:47:04] Found snpEff - /usr/local/bin/snpEff
[00:47:04] Found samclip - /usr/local/bin/samclip
[00:47:04] Found seqtk - /usr/local/bin/seqtk
[00:47:04] Found parallel - /usr/local/bin/parallel
[00:47:04] Found freebayes - /usr/local/bin/freebayes
[00:47:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:47:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:47:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:47:04] Found vcfuniq - /usr/local/bin/vcfuniq
[00:47:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:47:04] Found gzip - /bin/gzip
[00:47:04] Found vt - /usr/local/bin/vt
[00:47:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:47:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:47:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:47:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:47:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:47:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:47:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:47:05] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:17:33] This is snippy 4.6.0Show full stderr[01:17:33] This is snippy 4.6.0
[01:17:33] Written by Torsten Seemann
[01:17:33] Obtained from https://github.com/tseemann/snippy
[01:17:33] Detected operating system: linux
[01:17:33] Enabling bundled linux tools.
[01:17:33] Found bwa - /usr/local/bin/bwa
[01:17:33] Found bcftools - /usr/local/bin/bcftools
[01:17:33] Found samtools - /usr/local/bin/samtools
[01:17:33] Found java - /usr/local/bin/java
[01:17:33] Found snpEff - /usr/local/bin/snpEff
[01:17:33] Found samclip - /usr/local/bin/samclip
[01:17:33] Found seqtk - /usr/local/bin/seqtk
[01:17:33] Found parallel - /usr/local/bin/parallel
[01:17:33] Found freebayes - /usr/local/bin/freebayes
[01:17:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:17:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:17:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:17:33] Found vcfuniq - /usr/local/bin/vcfuniq
[01:17:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:17:33] Found gzip - /bin/gzip
[01:17:33] Found vt - /usr/local/bin/vt
[01:17:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:17:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:17:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:17:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:17:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:17:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:17:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:17:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:47:16] This is snippy 4.6.0Show full stderr[00:47:16] This is snippy 4.6.0
[00:47:16] Written by Torsten Seemann
[00:47:16] Obtained from https://github.com/tseemann/snippy
[00:47:16] Detected operating system: linux
[00:47:16] Enabling bundled linux tools.
[00:47:16] Found bwa - /usr/local/bin/bwa
[00:47:16] Found bcftools - /usr/local/bin/bcftools
[00:47:16] Found samtools - /usr/local/bin/samtools
[00:47:16] Found java - /usr/local/bin/java
[00:47:16] Found snpEff - /usr/local/bin/snpEff
[00:47:16] Found samclip - /usr/local/bin/samclip
[00:47:16] Found seqtk - /usr/local/bin/seqtk
[00:47:16] Found parallel - /usr/local/bin/parallel
[00:47:16] Found freebayes - /usr/local/bin/freebayes
[00:47:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:47:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:47:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:47:16] Found vcfuniq - /usr/local/bin/vcfuniq
[00:47:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:47:16] Found gzip - /bin/gzip
[00:47:16] Found vt - /usr/local/bin/vt
[00:47:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:47:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:47:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:47:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:47:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:47:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:47:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:47:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:17:51] This is snippy 4.6.0Show full stderr[01:17:51] This is snippy 4.6.0
[01:17:51] Written by Torsten Seemann
[01:17:51] Obtained from https://github.com/tseemann/snippy
[01:17:51] Detected operating system: linux
[01:17:51] Enabling bundled linux tools.
[01:17:51] Found bwa - /usr/local/bin/bwa
[01:17:51] Found bcftools - /usr/local/bin/bcftools
[01:17:51] Found samtools - /usr/local/bin/samtools
[01:17:51] Found java - /usr/local/bin/java
[01:17:51] Found snpEff - /usr/local/bin/snpEff
[01:17:51] Found samclip - /usr/local/bin/samclip
[01:17:51] Found seqtk - /usr/local/bin/seqtk
[01:17:51] Found parallel - /usr/local/bin/parallel
[01:17:51] Found freebayes - /usr/local/bin/freebayes
[01:17:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:17:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:17:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:17:51] Found vcfuniq - /usr/local/bin/vcfuniq
[01:17:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:17:51] Found gzip - /bin/gzip
[01:17:51] Found vt - /usr/local/bin/vt
[01:17:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:17:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:17:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:17:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:17:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:17:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:17:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:17:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:25:03] This is snippy 4.6.0Show full stderr[01:25:03] This is snippy 4.6.0
[01:25:03] Written by Torsten Seemann
[01:25:03] Obtained from https://github.com/tseemann/snippy
[01:25:03] Detected operating system: linux
[01:25:03] Enabling bundled linux tools.
[01:25:03] Found bwa - /usr/local/bin/bwa
[01:25:03] Found bcftools - /usr/local/bin/bcftools
[01:25:03] Found samtools - /usr/local/bin/samtools
[01:25:03] Found java - /usr/local/bin/java
[01:25:03] Found snpEff - /usr/local/bin/snpEff
[01:25:03] Found samclip - /usr/local/bin/samclip
[01:25:03] Found seqtk - /usr/local/bin/seqtk
[01:25:03] Found parallel - /usr/local/bin/parallel
[01:25:03] Found freebayes - /usr/local/bin/freebayes
[01:25:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:25:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:25:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:25:03] Found vcfuniq - /usr/local/bin/vcfuniq
[01:25:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:25:03] Found gzip - /bin/gzip
[01:25:03] Found vt - /usr/local/bin/vt
[01:25:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:25:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:25:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:25:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:25:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:25:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:25:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:25:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:59:48] This is snippy 4.6.0Show full stderr[00:59:48] This is snippy 4.6.0
[00:59:48] Written by Torsten Seemann
[00:59:48] Obtained from https://github.com/tseemann/snippy
[00:59:48] Detected operating system: linux
[00:59:48] Enabling bundled linux tools.
[00:59:48] Found bwa - /usr/local/bin/bwa
[00:59:48] Found bcftools - /usr/local/bin/bcftools
[00:59:48] Found samtools - /usr/local/bin/samtools
[00:59:48] Found java - /usr/local/bin/java
[00:59:48] Found snpEff - /usr/local/bin/snpEff
[00:59:48] Found samclip - /usr/local/bin/samclip
[00:59:48] Found seqtk - /usr/local/bin/seqtk
[00:59:48] Found parallel - /usr/local/bin/parallel
[00:59:48] Found freebayes - /usr/local/bin/freebayes
[00:59:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:59:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:59:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:59:48] Found vcfuniq - /usr/local/bin/vcfuniq
[00:59:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:59:48] Found gzip - /bin/gzip
[00:59:48] Found vt - /usr/local/bin/vt
[00:59:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:59:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:59:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:59:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:59:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:59:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:59:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:59:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:00:06] This is snippy 4.6.0Show full stderr[01:00:06] This is snippy 4.6.0
[01:00:06] Written by Torsten Seemann
[01:00:06] Obtained from https://github.com/tseemann/snippy
[01:00:06] Detected operating system: linux
[01:00:06] Enabling bundled linux tools.
[01:00:06] Found bwa - /usr/local/bin/bwa
[01:00:06] Found bcftools - /usr/local/bin/bcftools
[01:00:06] Found samtools - /usr/local/bin/samtools
[01:00:06] Found java - /usr/local/bin/java
[01:00:06] Found snpEff - /usr/local/bin/snpEff
[01:00:06] Found samclip - /usr/local/bin/samclip
[01:00:06] Found seqtk - /usr/local/bin/seqtk
[01:00:06] Found parallel - /usr/local/bin/parallel
[01:00:06] Found freebayes - /usr/local/bin/freebayes
[01:00:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:00:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:00:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:00:06] Found vcfuniq - /usr/local/bin/vcfuniq
[01:00:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:00:06] Found gzip - /bin/gzip
[01:00:06] Found vt - /usr/local/bin/vt
[01:00:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:00:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:00:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:00:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:00:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:00:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:00:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:00:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:37:48] This is snippy 4.6.0Show full stderr[01:37:48] This is snippy 4.6.0
[01:37:48] Written by Torsten Seemann
[01:37:48] Obtained from https://github.com/tseemann/snippy
[01:37:48] Detected operating system: linux
[01:37:48] Enabling bundled linux tools.
[01:37:48] Found bwa - /usr/local/bin/bwa
[01:37:48] Found bcftools - /usr/local/bin/bcftools
[01:37:48] Found samtools - /usr/local/bin/samtools
[01:37:48] Found java - /usr/local/bin/java
[01:37:48] Found snpEff - /usr/local/bin/snpEff
[01:37:48] Found samclip - /usr/local/bin/samclip
[01:37:48] Found seqtk - /usr/local/bin/seqtk
[01:37:48] Found parallel - /usr/local/bin/parallel
[01:37:48] Found freebayes - /usr/local/bin/freebayes
[01:37:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:37:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:37:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:37:48] Found vcfuniq - /usr/local/bin/vcfuniq
[01:37:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:37:48] Found gzip - /bin/gzip
[01:37:48] Found vt - /usr/local/bin/vt
[01:37:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:37:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:37:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:37:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:37:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:37:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:37:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:37:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:37:51] This is snippy 4.6.0Show full stderr[01:37:51] This is snippy 4.6.0
[01:37:51] Written by Torsten Seemann
[01:37:51] Obtained from https://github.com/tseemann/snippy
[01:37:51] Detected operating system: linux
[01:37:51] Enabling bundled linux tools.
[01:37:51] Found bwa - /usr/local/bin/bwa
[01:37:51] Found bcftools - /usr/local/bin/bcftools
[01:37:51] Found samtools - /usr/local/bin/samtools
[01:37:51] Found java - /usr/local/bin/java
[01:37:51] Found snpEff - /usr/local/bin/snpEff
[01:37:51] Found samclip - /usr/local/bin/samclip
[01:37:51] Found seqtk - /usr/local/bin/seqtk
[01:37:51] Found parallel - /usr/local/bin/parallel
[01:37:51] Found freebayes - /usr/local/bin/freebayes
[01:37:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:37:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:37:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:37:51] Found vcfuniq - /usr/local/bin/vcfuniq
[01:37:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:37:51] Found gzip - /bin/gzip
[01:37:51] Found vt - /usr/local/bin/vt
[01:37:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:37:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:37:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:37:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:37:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:37:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:37:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:37:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:44:01] This is snippy 4.6.0Show full stderr[01:44:01] This is snippy 4.6.0
[01:44:01] Written by Torsten Seemann
[01:44:01] Obtained from https://github.com/tseemann/snippy
[01:44:01] Detected operating system: linux
[01:44:01] Enabling bundled linux tools.
[01:44:01] Found bwa - /usr/local/bin/bwa
[01:44:01] Found bcftools - /usr/local/bin/bcftools
[01:44:01] Found samtools - /usr/local/bin/samtools
[01:44:01] Found java - /usr/local/bin/java
[01:44:01] Found snpEff - /usr/local/bin/snpEff
[01:44:01] Found samclip - /usr/local/bin/samclip
[01:44:01] Found seqtk - /usr/local/bin/seqtk
[01:44:01] Found parallel - /usr/local/bin/parallel
[01:44:01] Found freebayes - /usr/local/bin/freebayes
[01:44:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:44:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:44:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:44:01] Found vcfuniq - /usr/local/bin/vcfuniq
[01:44:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:44:01] Found gzip - /bin/gzip
[01:44:01] Found vt - /usr/local/bin/vt
[01:44:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:44:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:44:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:44:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:44:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:44:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:44:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:44:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:05:13] This is snippy 4.6.0Show full stderr[01:05:13] This is snippy 4.6.0
[01:05:13] Written by Torsten Seemann
[01:05:13] Obtained from https://github.com/tseemann/snippy
[01:05:13] Detected operating system: linux
[01:05:13] Enabling bundled linux tools.
[01:05:13] Found bwa - /usr/local/bin/bwa
[01:05:13] Found bcftools - /usr/local/bin/bcftools
[01:05:13] Found samtools - /usr/local/bin/samtools
[01:05:13] Found java - /usr/local/bin/java
[01:05:13] Found snpEff - /usr/local/bin/snpEff
[01:05:13] Found samclip - /usr/local/bin/samclip
[01:05:13] Found seqtk - /usr/local/bin/seqtk
[01:05:13] Found parallel - /usr/local/bin/parallel
[01:05:13] Found freebayes - /usr/local/bin/freebayes
[01:05:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:05:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:05:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:05:13] Found vcfuniq - /usr/local/bin/vcfuniq
[01:05:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:05:13] Found gzip - /bin/gzip
[01:05:13] Found vt - /usr/local/bin/vt
[01:05:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:05:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:05:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:05:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:05:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:05:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:05:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:05:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:05:48] This is snippy 4.6.0Show full stderr[01:05:48] This is snippy 4.6.0
[01:05:48] Written by Torsten Seemann
[01:05:48] Obtained from https://github.com/tseemann/snippy
[01:05:48] Detected operating system: linux
[01:05:48] Enabling bundled linux tools.
[01:05:48] Found bwa - /usr/local/bin/bwa
[01:05:48] Found bcftools - /usr/local/bin/bcftools
[01:05:48] Found samtools - /usr/local/bin/samtools
[01:05:48] Found java - /usr/local/bin/java
[01:05:48] Found snpEff - /usr/local/bin/snpEff
[01:05:48] Found samclip - /usr/local/bin/samclip
[01:05:48] Found seqtk - /usr/local/bin/seqtk
[01:05:48] Found parallel - /usr/local/bin/parallel
[01:05:48] Found freebayes - /usr/local/bin/freebayes
[01:05:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:05:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:05:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:05:48] Found vcfuniq - /usr/local/bin/vcfuniq
[01:05:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:05:48] Found gzip - /bin/gzip
[01:05:48] Found vt - /usr/local/bin/vt
[01:05:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:05:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:05:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:05:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:05:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:05:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:05:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:05:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:45:57] This is snippy 4.6.0Show full stderr[01:45:57] This is snippy 4.6.0
[01:45:57] Written by Torsten Seemann
[01:45:57] Obtained from https://github.com/tseemann/snippy
[01:45:57] Detected operating system: linux
[01:45:57] Enabling bundled linux tools.
[01:45:57] Found bwa - /usr/local/bin/bwa
[01:45:57] Found bcftools - /usr/local/bin/bcftools
[01:45:57] Found samtools - /usr/local/bin/samtools
[01:45:57] Found java - /usr/local/bin/java
[01:45:57] Found snpEff - /usr/local/bin/snpEff
[01:45:57] Found samclip - /usr/local/bin/samclip
[01:45:57] Found seqtk - /usr/local/bin/seqtk
[01:45:57] Found parallel - /usr/local/bin/parallel
[01:45:57] Found freebayes - /usr/local/bin/freebayes
[01:45:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:45:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:45:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:45:57] Found vcfuniq - /usr/local/bin/vcfuniq
[01:45:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:45:57] Found gzip - /bin/gzip
[01:45:57] Found vt - /usr/local/bin/vt
[01:45:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:45:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:45:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:45:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:45:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:45:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:45:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:45:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:09:16] This is snippy 4.6.0Show full stderr[01:09:16] This is snippy 4.6.0
[01:09:16] Written by Torsten Seemann
[01:09:16] Obtained from https://github.com/tseemann/snippy
[01:09:16] Detected operating system: linux
[01:09:16] Enabling bundled linux tools.
[01:09:16] Found bwa - /usr/local/bin/bwa
[01:09:16] Found bcftools - /usr/local/bin/bcftools
[01:09:16] Found samtools - /usr/local/bin/samtools
[01:09:16] Found java - /usr/local/bin/java
[01:09:16] Found snpEff - /usr/local/bin/snpEff
[01:09:16] Found samclip - /usr/local/bin/samclip
[01:09:16] Found seqtk - /usr/local/bin/seqtk
[01:09:16] Found parallel - /usr/local/bin/parallel
[01:09:16] Found freebayes - /usr/local/bin/freebayes
[01:09:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:09:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:09:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:09:16] Found vcfuniq - /usr/local/bin/vcfuniq
[01:09:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:09:16] Found gzip - /bin/gzip
[01:09:16] Found vt - /usr/local/bin/vt
[01:09:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:09:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:09:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:09:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:09:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:09:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:09:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:09:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:33:08] This is snippy 4.6.0Show full stderr[01:33:08] This is snippy 4.6.0
[01:33:08] Written by Torsten Seemann
[01:33:08] Obtained from https://github.com/tseemann/snippy
[01:33:08] Detected operating system: linux
[01:33:08] Enabling bundled linux tools.
[01:33:08] Found bwa - /usr/local/bin/bwa
[01:33:08] Found bcftools - /usr/local/bin/bcftools
[01:33:08] Found samtools - /usr/local/bin/samtools
[01:33:08] Found java - /usr/local/bin/java
[01:33:08] Found snpEff - /usr/local/bin/snpEff
[01:33:08] Found samclip - /usr/local/bin/samclip
[01:33:08] Found seqtk - /usr/local/bin/seqtk
[01:33:08] Found parallel - /usr/local/bin/parallel
[01:33:08] Found freebayes - /usr/local/bin/freebayes
[01:33:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:33:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:33:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:33:08] Found vcfuniq - /usr/local/bin/vcfuniq
[01:33:08] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:33:08] Found gzip - /bin/gzip
[01:33:08] Found vt - /usr/local/bin/vt
[01:33:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:33:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:33:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:33:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:33:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:33:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:33:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:33:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:23:15] This is snippy 4.6.0Show full stderr[01:23:15] This is snippy 4.6.0
[01:23:15] Written by Torsten Seemann
[01:23:15] Obtained from https://github.com/tseemann/snippy
[01:23:15] Detected operating system: linux
[01:23:15] Enabling bundled linux tools.
[01:23:15] Found bwa - /usr/local/bin/bwa
[01:23:15] Found bcftools - /usr/local/bin/bcftools
[01:23:15] Found samtools - /usr/local/bin/samtools
[01:23:15] Found java - /usr/local/bin/java
[01:23:15] Found snpEff - /usr/local/bin/snpEff
[01:23:15] Found samclip - /usr/local/bin/samclip
[01:23:15] Found seqtk - /usr/local/bin/seqtk
[01:23:15] Found parallel - /usr/local/bin/parallel
[01:23:15] Found freebayes - /usr/local/bin/freebayes
[01:23:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:23:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:23:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:23:15] Found vcfuniq - /usr/local/bin/vcfuniq
[01:23:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:23:15] Found gzip - /bin/gzip
[01:23:15] Found vt - /usr/local/bin/vt
[01:23:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:23:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:23:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:23:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:23:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:23:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:23:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:23:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:23:42] This is snippy 4.6.0Show full stderr[01:23:42] This is snippy 4.6.0
[01:23:42] Written by Torsten Seemann
[01:23:42] Obtained from https://github.com/tseemann/snippy
[01:23:42] Detected operating system: linux
[01:23:42] Enabling bundled linux tools.
[01:23:42] Found bwa - /usr/local/bin/bwa
[01:23:42] Found bcftools - /usr/local/bin/bcftools
[01:23:42] Found samtools - /usr/local/bin/samtools
[01:23:42] Found java - /usr/local/bin/java
[01:23:42] Found snpEff - /usr/local/bin/snpEff
[01:23:42] Found samclip - /usr/local/bin/samclip
[01:23:42] Found seqtk - /usr/local/bin/seqtk
[01:23:42] Found parallel - /usr/local/bin/parallel
[01:23:42] Found freebayes - /usr/local/bin/freebayes
[01:23:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:23:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:23:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:23:42] Found vcfuniq - /usr/local/bin/vcfuniq
[01:23:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:23:43] Found gzip - /bin/gzip
[01:23:43] Found vt - /usr/local/bin/vt
[01:23:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:23:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:23:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:23:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:23:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:23:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:23:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:23:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:24:18] This is snippy 4.6.0Show full stderr[01:24:18] This is snippy 4.6.0
[01:24:18] Written by Torsten Seemann
[01:24:18] Obtained from https://github.com/tseemann/snippy
[01:24:18] Detected operating system: linux
[01:24:18] Enabling bundled linux tools.
[01:24:18] Found bwa - /usr/local/bin/bwa
[01:24:18] Found bcftools - /usr/local/bin/bcftools
[01:24:18] Found samtools - /usr/local/bin/samtools
[01:24:18] Found java - /usr/local/bin/java
[01:24:18] Found snpEff - /usr/local/bin/snpEff
[01:24:18] Found samclip - /usr/local/bin/samclip
[01:24:18] Found seqtk - /usr/local/bin/seqtk
[01:24:18] Found parallel - /usr/local/bin/parallel
[01:24:18] Found freebayes - /usr/local/bin/freebayes
[01:24:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:24:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:24:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:24:18] Found vcfuniq - /usr/local/bin/vcfuniq
[01:24:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:24:18] Found gzip - /bin/gzip
[01:24:18] Found vt - /usr/local/bin/vt
[01:24:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:24:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:24:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:24:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:24:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:24:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:24:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:24:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:24:45] This is snippy 4.6.0Show full stderr[01:24:45] This is snippy 4.6.0
[01:24:45] Written by Torsten Seemann
[01:24:45] Obtained from https://github.com/tseemann/snippy
[01:24:45] Detected operating system: linux
[01:24:45] Enabling bundled linux tools.
[01:24:45] Found bwa - /usr/local/bin/bwa
[01:24:45] Found bcftools - /usr/local/bin/bcftools
[01:24:45] Found samtools - /usr/local/bin/samtools
[01:24:45] Found java - /usr/local/bin/java
[01:24:45] Found snpEff - /usr/local/bin/snpEff
[01:24:45] Found samclip - /usr/local/bin/samclip
[01:24:45] Found seqtk - /usr/local/bin/seqtk
[01:24:45] Found parallel - /usr/local/bin/parallel
[01:24:45] Found freebayes - /usr/local/bin/freebayes
[01:24:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:24:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:24:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:24:45] Found vcfuniq - /usr/local/bin/vcfuniq
[01:24:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:24:45] Found gzip - /bin/gzip
[01:24:45] Found vt - /usr/local/bin/vt
[01:24:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:24:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:24:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:24:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:24:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:24:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:24:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:24:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:36:49] This is snippy 4.6.0Show full stderr[01:36:49] This is snippy 4.6.0
[01:36:49] Written by Torsten Seemann
[01:36:49] Obtained from https://github.com/tseemann/snippy
[01:36:49] Detected operating system: linux
[01:36:49] Enabling bundled linux tools.
[01:36:49] Found bwa - /usr/local/bin/bwa
[01:36:49] Found bcftools - /usr/local/bin/bcftools
[01:36:49] Found samtools - /usr/local/bin/samtools
[01:36:49] Found java - /usr/local/bin/java
[01:36:49] Found snpEff - /usr/local/bin/snpEff
[01:36:49] Found samclip - /usr/local/bin/samclip
[01:36:49] Found seqtk - /usr/local/bin/seqtk
[01:36:49] Found parallel - /usr/local/bin/parallel
[01:36:49] Found freebayes - /usr/local/bin/freebayes
[01:36:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:36:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:36:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:36:49] Found vcfuniq - /usr/local/bin/vcfuniq
[01:36:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:36:49] Found gzip - /bin/gzip
[01:36:49] Found vt - /usr/local/bin/vt
[01:36:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:36:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:36:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:36:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:36:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:36:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:36:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:36:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:24:57] This is snippy 4.6.0Show full stderr[01:24:57] This is snippy 4.6.0
[01:24:57] Written by Torsten Seemann
[01:24:57] Obtained from https://github.com/tseemann/snippy
[01:24:57] Detected operating system: linux
[01:24:57] Enabling bundled linux tools.
[01:24:57] Found bwa - /usr/local/bin/bwa
[01:24:57] Found bcftools - /usr/local/bin/bcftools
[01:24:57] Found samtools - /usr/local/bin/samtools
[01:24:57] Found java - /usr/local/bin/java
[01:24:57] Found snpEff - /usr/local/bin/snpEff
[01:24:57] Found samclip - /usr/local/bin/samclip
[01:24:57] Found seqtk - /usr/local/bin/seqtk
[01:24:57] Found parallel - /usr/local/bin/parallel
[01:24:58] Found freebayes - /usr/local/bin/freebayes
[01:24:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:24:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:24:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:24:58] Found vcfuniq - /usr/local/bin/vcfuniq
[01:24:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:24:58] Found gzip - /bin/gzip
[01:24:58] Found vt - /usr/local/bin/vt
[01:24:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:24:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:24:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:24:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:24:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:24:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:24:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:24:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:39:13] This is snippy 4.6.0Show full stderr[01:39:13] This is snippy 4.6.0
[01:39:13] Written by Torsten Seemann
[01:39:13] Obtained from https://github.com/tseemann/snippy
[01:39:13] Detected operating system: linux
[01:39:13] Enabling bundled linux tools.
[01:39:13] Found bwa - /usr/local/bin/bwa
[01:39:13] Found bcftools - /usr/local/bin/bcftools
[01:39:13] Found samtools - /usr/local/bin/samtools
[01:39:13] Found java - /usr/local/bin/java
[01:39:13] Found snpEff - /usr/local/bin/snpEff
[01:39:13] Found samclip - /usr/local/bin/samclip
[01:39:13] Found seqtk - /usr/local/bin/seqtk
[01:39:13] Found parallel - /usr/local/bin/parallel
[01:39:13] Found freebayes - /usr/local/bin/freebayes
[01:39:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:39:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:39:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:39:13] Found vcfuniq - /usr/local/bin/vcfuniq
[01:39:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:39:13] Found gzip - /bin/gzip
[01:39:13] Found vt - /usr/local/bin/vt
[01:39:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:39:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:39:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:39:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:39:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:39:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:39:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:39:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:25:01] This is snippy 4.6.0Show full stderr[01:25:01] This is snippy 4.6.0
[01:25:01] Written by Torsten Seemann
[01:25:01] Obtained from https://github.com/tseemann/snippy
[01:25:01] Detected operating system: linux
[01:25:01] Enabling bundled linux tools.
[01:25:01] Found bwa - /usr/local/bin/bwa
[01:25:01] Found bcftools - /usr/local/bin/bcftools
[01:25:01] Found samtools - /usr/local/bin/samtools
[01:25:01] Found java - /usr/local/bin/java
[01:25:01] Found snpEff - /usr/local/bin/snpEff
[01:25:01] Found samclip - /usr/local/bin/samclip
[01:25:01] Found seqtk - /usr/local/bin/seqtk
[01:25:01] Found parallel - /usr/local/bin/parallel
[01:25:01] Found freebayes - /usr/local/bin/freebayes
[01:25:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:25:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:25:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:25:01] Found vcfuniq - /usr/local/bin/vcfuniq
[01:25:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:25:01] Found gzip - /bin/gzip
[01:25:01] Found vt - /usr/local/bin/vt
[01:25:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:25:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:25:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:25:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:25:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:25:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:25:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:25:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:25:07] This is snippy 4.6.0Show full stderr[01:25:07] This is snippy 4.6.0
[01:25:07] Written by Torsten Seemann
[01:25:07] Obtained from https://github.com/tseemann/snippy
[01:25:07] Detected operating system: linux
[01:25:07] Enabling bundled linux tools.
[01:25:07] Found bwa - /usr/local/bin/bwa
[01:25:07] Found bcftools - /usr/local/bin/bcftools
[01:25:07] Found samtools - /usr/local/bin/samtools
[01:25:07] Found java - /usr/local/bin/java
[01:25:07] Found snpEff - /usr/local/bin/snpEff
[01:25:07] Found samclip - /usr/local/bin/samclip
[01:25:07] Found seqtk - /usr/local/bin/seqtk
[01:25:07] Found parallel - /usr/local/bin/parallel
[01:25:07] Found freebayes - /usr/local/bin/freebayes
[01:25:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:25:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:25:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:25:07] Found vcfuniq - /usr/local/bin/vcfuniq
[01:25:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:25:07] Found gzip - /bin/gzip
[01:25:07] Found vt - /usr/local/bin/vt
[01:25:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:25:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:25:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:25:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:25:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:25:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:25:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:25:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:25:12] This is snippy 4.6.0Show full stderr[01:25:12] This is snippy 4.6.0
[01:25:12] Written by Torsten Seemann
[01:25:12] Obtained from https://github.com/tseemann/snippy
[01:25:12] Detected operating system: linux
[01:25:12] Enabling bundled linux tools.
[01:25:12] Found bwa - /usr/local/bin/bwa
[01:25:12] Found bcftools - /usr/local/bin/bcftools
[01:25:12] Found samtools - /usr/local/bin/samtools
[01:25:12] Found java - /usr/local/bin/java
[01:25:12] Found snpEff - /usr/local/bin/snpEff
[01:25:12] Found samclip - /usr/local/bin/samclip
[01:25:12] Found seqtk - /usr/local/bin/seqtk
[01:25:12] Found parallel - /usr/local/bin/parallel
[01:25:12] Found freebayes - /usr/local/bin/freebayes
[01:25:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:25:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:25:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:25:12] Found vcfuniq - /usr/local/bin/vcfuniq
[01:25:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:25:12] Found gzip - /bin/gzip
[01:25:12] Found vt - /usr/local/bin/vt
[01:25:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:25:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:25:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:25:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:25:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:25:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:25:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:25:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:25:30] This is snippy 4.6.0Show full stderr[01:25:30] This is snippy 4.6.0
[01:25:30] Written by Torsten Seemann
[01:25:30] Obtained from https://github.com/tseemann/snippy
[01:25:30] Detected operating system: linux
[01:25:30] Enabling bundled linux tools.
[01:25:30] Found bwa - /usr/local/bin/bwa
[01:25:30] Found bcftools - /usr/local/bin/bcftools
[01:25:30] Found samtools - /usr/local/bin/samtools
[01:25:30] Found java - /usr/local/bin/java
[01:25:30] Found snpEff - /usr/local/bin/snpEff
[01:25:30] Found samclip - /usr/local/bin/samclip
[01:25:30] Found seqtk - /usr/local/bin/seqtk
[01:25:30] Found parallel - /usr/local/bin/parallel
[01:25:30] Found freebayes - /usr/local/bin/freebayes
[01:25:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:25:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:25:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:25:30] Found vcfuniq - /usr/local/bin/vcfuniq
[01:25:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:25:30] Found gzip - /bin/gzip
[01:25:30] Found vt - /usr/local/bin/vt
[01:25:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:25:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:25:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:25:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:25:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:25:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:25:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:25:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:25:28] This is snippy 4.6.0Show full stderr[01:25:28] This is snippy 4.6.0
[01:25:28] Written by Torsten Seemann
[01:25:28] Obtained from https://github.com/tseemann/snippy
[01:25:28] Detected operating system: linux
[01:25:28] Enabling bundled linux tools.
[01:25:28] Found bwa - /usr/local/bin/bwa
[01:25:28] Found bcftools - /usr/local/bin/bcftools
[01:25:28] Found samtools - /usr/local/bin/samtools
[01:25:28] Found java - /usr/local/bin/java
[01:25:28] Found snpEff - /usr/local/bin/snpEff
[01:25:28] Found samclip - /usr/local/bin/samclip
[01:25:28] Found seqtk - /usr/local/bin/seqtk
[01:25:28] Found parallel - /usr/local/bin/parallel
[01:25:28] Found freebayes - /usr/local/bin/freebayes
[01:25:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:25:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:25:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:25:28] Found vcfuniq - /usr/local/bin/vcfuniq
[01:25:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:25:28] Found gzip - /bin/gzip
[01:25:28] Found vt - /usr/local/bin/vt
[01:25:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:25:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:25:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:25:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:25:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:25:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:25:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:25:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:45:18] This is snippy 4.6.0Show full stderr[01:45:18] This is snippy 4.6.0
[01:45:18] Written by Torsten Seemann
[01:45:18] Obtained from https://github.com/tseemann/snippy
[01:45:18] Detected operating system: linux
[01:45:18] Enabling bundled linux tools.
[01:45:18] Found bwa - /usr/local/bin/bwa
[01:45:18] Found bcftools - /usr/local/bin/bcftools
[01:45:18] Found samtools - /usr/local/bin/samtools
[01:45:18] Found java - /usr/local/bin/java
[01:45:18] Found snpEff - /usr/local/bin/snpEff
[01:45:18] Found samclip - /usr/local/bin/samclip
[01:45:18] Found seqtk - /usr/local/bin/seqtk
[01:45:18] Found parallel - /usr/local/bin/parallel
[01:45:18] Found freebayes - /usr/local/bin/freebayes
[01:45:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:45:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:45:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:45:18] Found vcfuniq - /usr/local/bin/vcfuniq
[01:45:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:45:18] Found gzip - /bin/gzip
[01:45:18] Found vt - /usr/local/bin/vt
[01:45:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:45:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:45:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:45:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:45:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:45:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:45:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:45:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:25:48] This is snippy 4.6.0Show full stderr[01:25:48] This is snippy 4.6.0
[01:25:48] Written by Torsten Seemann
[01:25:48] Obtained from https://github.com/tseemann/snippy
[01:25:48] Detected operating system: linux
[01:25:48] Enabling bundled linux tools.
[01:25:48] Found bwa - /usr/local/bin/bwa
[01:25:48] Found bcftools - /usr/local/bin/bcftools
[01:25:48] Found samtools - /usr/local/bin/samtools
[01:25:48] Found java - /usr/local/bin/java
[01:25:48] Found snpEff - /usr/local/bin/snpEff
[01:25:48] Found samclip - /usr/local/bin/samclip
[01:25:48] Found seqtk - /usr/local/bin/seqtk
[01:25:48] Found parallel - /usr/local/bin/parallel
[01:25:48] Found freebayes - /usr/local/bin/freebayes
[01:25:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:25:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:25:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:25:48] Found vcfuniq - /usr/local/bin/vcfuniq
[01:25:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:25:48] Found gzip - /bin/gzip
[01:25:48] Found vt - /usr/local/bin/vt
[01:25:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:25:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:25:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:25:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:25:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:25:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:25:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:25:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:26:09] This is snippy 4.6.0Show full stderr[01:26:09] This is snippy 4.6.0
[01:26:09] Written by Torsten Seemann
[01:26:09] Obtained from https://github.com/tseemann/snippy
[01:26:09] Detected operating system: linux
[01:26:09] Enabling bundled linux tools.
[01:26:09] Found bwa - /usr/local/bin/bwa
[01:26:09] Found bcftools - /usr/local/bin/bcftools
[01:26:09] Found samtools - /usr/local/bin/samtools
[01:26:09] Found java - /usr/local/bin/java
[01:26:09] Found snpEff - /usr/local/bin/snpEff
[01:26:09] Found samclip - /usr/local/bin/samclip
[01:26:09] Found seqtk - /usr/local/bin/seqtk
[01:26:09] Found parallel - /usr/local/bin/parallel
[01:26:09] Found freebayes - /usr/local/bin/freebayes
[01:26:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:26:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:26:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:26:09] Found vcfuniq - /usr/local/bin/vcfuniq
[01:26:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:26:09] Found gzip - /bin/gzip
[01:26:09] Found vt - /usr/local/bin/vt
[01:26:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:26:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:26:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:26:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:26:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:26:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:26:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:26:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:33:14] This is snippy 4.6.0Show full stderr[00:33:14] This is snippy 4.6.0
[00:33:14] Written by Torsten Seemann
[00:33:14] Obtained from https://github.com/tseemann/snippy
[00:33:14] Detected operating system: linux
[00:33:14] Enabling bundled linux tools.
[00:33:14] Found bwa - /usr/local/bin/bwa
[00:33:14] Found bcftools - /usr/local/bin/bcftools
[00:33:14] Found samtools - /usr/local/bin/samtools
[00:33:14] Found java - /usr/local/bin/java
[00:33:14] Found snpEff - /usr/local/bin/snpEff
[00:33:14] Found samclip - /usr/local/bin/samclip
[00:33:14] Found seqtk - /usr/local/bin/seqtk
[00:33:14] Found parallel - /usr/local/bin/parallel
[00:33:14] Found freebayes - /usr/local/bin/freebayes
[00:33:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:14] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:14] Found gzip - /bin/gzip
[00:33:14] Found vt - /usr/local/bin/vt
[00:33:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:15] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:58:50] This is snippy 4.6.0Show full stderr[00:58:50] This is snippy 4.6.0
[00:58:50] Written by Torsten Seemann
[00:58:50] Obtained from https://github.com/tseemann/snippy
[00:58:50] Detected operating system: linux
[00:58:50] Enabling bundled linux tools.
[00:58:50] Found bwa - /usr/local/bin/bwa
[00:58:50] Found bcftools - /usr/local/bin/bcftools
[00:58:50] Found samtools - /usr/local/bin/samtools
[00:58:50] Found java - /usr/local/bin/java
[00:58:50] Found snpEff - /usr/local/bin/snpEff
[00:58:50] Found samclip - /usr/local/bin/samclip
[00:58:50] Found seqtk - /usr/local/bin/seqtk
[00:58:50] Found parallel - /usr/local/bin/parallel
[00:58:50] Found freebayes - /usr/local/bin/freebayes
[00:58:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:58:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:58:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:58:50] Found vcfuniq - /usr/local/bin/vcfuniq
[00:58:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:58:50] Found gzip - /bin/gzip
[00:58:50] Found vt - /usr/local/bin/vt
[00:58:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:58:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:58:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:58:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:58:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:58:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:58:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:58:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:33:24] This is snippy 4.6.0Show full stderr[00:33:24] This is snippy 4.6.0
[00:33:24] Written by Torsten Seemann
[00:33:24] Obtained from https://github.com/tseemann/snippy
[00:33:24] Detected operating system: linux
[00:33:24] Enabling bundled linux tools.
[00:33:24] Found bwa - /usr/local/bin/bwa
[00:33:24] Found bcftools - /usr/local/bin/bcftools
[00:33:24] Found samtools - /usr/local/bin/samtools
[00:33:24] Found java - /usr/local/bin/java
[00:33:24] Found snpEff - /usr/local/bin/snpEff
[00:33:24] Found samclip - /usr/local/bin/samclip
[00:33:24] Found seqtk - /usr/local/bin/seqtk
[00:33:24] Found parallel - /usr/local/bin/parallel
[00:33:24] Found freebayes - /usr/local/bin/freebayes
[00:33:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:24] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:24] Found gzip - /bin/gzip
[00:33:24] Found vt - /usr/local/bin/vt
[00:33:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:33:39] This is snippy 4.6.0Show full stderr[00:33:39] This is snippy 4.6.0
[00:33:39] Written by Torsten Seemann
[00:33:39] Obtained from https://github.com/tseemann/snippy
[00:33:39] Detected operating system: linux
[00:33:39] Enabling bundled linux tools.
[00:33:39] Found bwa - /usr/local/bin/bwa
[00:33:39] Found bcftools - /usr/local/bin/bcftools
[00:33:39] Found samtools - /usr/local/bin/samtools
[00:33:39] Found java - /usr/local/bin/java
[00:33:39] Found snpEff - /usr/local/bin/snpEff
[00:33:39] Found samclip - /usr/local/bin/samclip
[00:33:39] Found seqtk - /usr/local/bin/seqtk
[00:33:39] Found parallel - /usr/local/bin/parallel
[00:33:39] Found freebayes - /usr/local/bin/freebayes
[00:33:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:39] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:39] Found gzip - /bin/gzip
[00:33:39] Found vt - /usr/local/bin/vt
[00:33:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:35:12] This is snippy 4.6.0Show full stderr[00:35:12] This is snippy 4.6.0
[00:35:12] Written by Torsten Seemann
[00:35:12] Obtained from https://github.com/tseemann/snippy
[00:35:12] Detected operating system: linux
[00:35:12] Enabling bundled linux tools.
[00:35:12] Found bwa - /usr/local/bin/bwa
[00:35:12] Found bcftools - /usr/local/bin/bcftools
[00:35:12] Found samtools - /usr/local/bin/samtools
[00:35:12] Found java - /usr/local/bin/java
[00:35:12] Found snpEff - /usr/local/bin/snpEff
[00:35:12] Found samclip - /usr/local/bin/samclip
[00:35:12] Found seqtk - /usr/local/bin/seqtk
[00:35:12] Found parallel - /usr/local/bin/parallel
[00:35:13] Found freebayes - /usr/local/bin/freebayes
[00:35:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:35:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:35:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:35:13] Found vcfuniq - /usr/local/bin/vcfuniq
[00:35:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:35:13] Found gzip - /bin/gzip
[00:35:13] Found vt - /usr/local/bin/vt
[00:35:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:35:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:35:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:35:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:35:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:35:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:35:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:35:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:35:26] This is snippy 4.6.0Show full stderr[00:35:26] This is snippy 4.6.0
[00:35:26] Written by Torsten Seemann
[00:35:26] Obtained from https://github.com/tseemann/snippy
[00:35:26] Detected operating system: linux
[00:35:26] Enabling bundled linux tools.
[00:35:26] Found bwa - /usr/local/bin/bwa
[00:35:26] Found bcftools - /usr/local/bin/bcftools
[00:35:26] Found samtools - /usr/local/bin/samtools
[00:35:26] Found java - /usr/local/bin/java
[00:35:26] Found snpEff - /usr/local/bin/snpEff
[00:35:26] Found samclip - /usr/local/bin/samclip
[00:35:26] Found seqtk - /usr/local/bin/seqtk
[00:35:26] Found parallel - /usr/local/bin/parallel
[00:35:26] Found freebayes - /usr/local/bin/freebayes
[00:35:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:35:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:35:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:35:26] Found vcfuniq - /usr/local/bin/vcfuniq
[00:35:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:35:26] Found gzip - /bin/gzip
[00:35:26] Found vt - /usr/local/bin/vt
[00:35:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:35:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:35:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:35:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:35:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:35:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:35:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:35:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:33:53] This is snippy 4.6.0Show full stderr[00:33:53] This is snippy 4.6.0
[00:33:53] Written by Torsten Seemann
[00:33:53] Obtained from https://github.com/tseemann/snippy
[00:33:53] Detected operating system: linux
[00:33:53] Enabling bundled linux tools.
[00:33:53] Found bwa - /usr/local/bin/bwa
[00:33:53] Found bcftools - /usr/local/bin/bcftools
[00:33:53] Found samtools - /usr/local/bin/samtools
[00:33:53] Found java - /usr/local/bin/java
[00:33:53] Found snpEff - /usr/local/bin/snpEff
[00:33:53] Found samclip - /usr/local/bin/samclip
[00:33:53] Found seqtk - /usr/local/bin/seqtk
[00:33:53] Found parallel - /usr/local/bin/parallel
[00:33:53] Found freebayes - /usr/local/bin/freebayes
[00:33:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:53] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:53] Found gzip - /bin/gzip
[00:33:53] Found vt - /usr/local/bin/vt
[00:33:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:33:57] This is snippy 4.6.0Show full stderr[00:33:57] This is snippy 4.6.0
[00:33:57] Written by Torsten Seemann
[00:33:57] Obtained from https://github.com/tseemann/snippy
[00:33:57] Detected operating system: linux
[00:33:57] Enabling bundled linux tools.
[00:33:57] Found bwa - /usr/local/bin/bwa
[00:33:57] Found bcftools - /usr/local/bin/bcftools
[00:33:57] Found samtools - /usr/local/bin/samtools
[00:33:57] Found java - /usr/local/bin/java
[00:33:57] Found snpEff - /usr/local/bin/snpEff
[00:33:57] Found samclip - /usr/local/bin/samclip
[00:33:57] Found seqtk - /usr/local/bin/seqtk
[00:33:57] Found parallel - /usr/local/bin/parallel
[00:33:57] Found freebayes - /usr/local/bin/freebayes
[00:33:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:33:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:33:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:33:57] Found vcfuniq - /usr/local/bin/vcfuniq
[00:33:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:33:57] Found gzip - /bin/gzip
[00:33:57] Found vt - /usr/local/bin/vt
[00:33:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:33:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:33:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:33:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:33:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:33:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:33:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:33:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:35:55] This is snippy 4.6.0Show full stderr[00:35:55] This is snippy 4.6.0
[00:35:55] Written by Torsten Seemann
[00:35:55] Obtained from https://github.com/tseemann/snippy
[00:35:55] Detected operating system: linux
[00:35:55] Enabling bundled linux tools.
[00:35:55] Found bwa - /usr/local/bin/bwa
[00:35:55] Found bcftools - /usr/local/bin/bcftools
[00:35:55] Found samtools - /usr/local/bin/samtools
[00:35:55] Found java - /usr/local/bin/java
[00:35:55] Found snpEff - /usr/local/bin/snpEff
[00:35:55] Found samclip - /usr/local/bin/samclip
[00:35:55] Found seqtk - /usr/local/bin/seqtk
[00:35:55] Found parallel - /usr/local/bin/parallel
[00:35:55] Found freebayes - /usr/local/bin/freebayes
[00:35:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:35:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:35:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:35:55] Found vcfuniq - /usr/local/bin/vcfuniq
[00:35:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:35:55] Found gzip - /bin/gzip
[00:35:55] Found vt - /usr/local/bin/vt
[00:35:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:35:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:35:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:35:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:35:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:35:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:35:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:35:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:36:09] This is snippy 4.6.0Show full stderr[00:36:09] This is snippy 4.6.0
[00:36:09] Written by Torsten Seemann
[00:36:09] Obtained from https://github.com/tseemann/snippy
[00:36:09] Detected operating system: linux
[00:36:09] Enabling bundled linux tools.
[00:36:09] Found bwa - /usr/local/bin/bwa
[00:36:09] Found bcftools - /usr/local/bin/bcftools
[00:36:09] Found samtools - /usr/local/bin/samtools
[00:36:09] Found java - /usr/local/bin/java
[00:36:09] Found snpEff - /usr/local/bin/snpEff
[00:36:09] Found samclip - /usr/local/bin/samclip
[00:36:09] Found seqtk - /usr/local/bin/seqtk
[00:36:09] Found parallel - /usr/local/bin/parallel
[00:36:09] Found freebayes - /usr/local/bin/freebayes
[00:36:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:36:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:36:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:36:09] Found vcfuniq - /usr/local/bin/vcfuniq
[00:36:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:36:09] Found gzip - /bin/gzip
[00:36:09] Found vt - /usr/local/bin/vt
[00:36:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:36:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:36:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:36:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:36:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:36:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:36:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:36:09] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:41:47] This is snippy 4.6.0Show full stderr[00:41:47] This is snippy 4.6.0
[00:41:47] Written by Torsten Seemann
[00:41:47] Obtained from https://github.com/tseemann/snippy
[00:41:47] Detected operating system: linux
[00:41:47] Enabling bundled linux tools.
[00:41:47] Found bwa - /usr/local/bin/bwa
[00:41:47] Found bcftools - /usr/local/bin/bcftools
[00:41:47] Found samtools - /usr/local/bin/samtools
[00:41:47] Found java - /usr/local/bin/java
[00:41:47] Found snpEff - /usr/local/bin/snpEff
[00:41:48] Found samclip - /usr/local/bin/samclip
[00:41:48] Found seqtk - /usr/local/bin/seqtk
[00:41:48] Found parallel - /usr/local/bin/parallel
[00:41:48] Found freebayes - /usr/local/bin/freebayes
[00:41:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:41:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:41:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:41:48] Found vcfuniq - /usr/local/bin/vcfuniq
[00:41:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:41:48] Found gzip - /bin/gzip
[00:41:48] Found vt - /usr/local/bin/vt
[00:41:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:41:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:41:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:41:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:41:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:41:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:41:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:41:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:34:09] This is snippy 4.6.0Show full stderr[00:34:09] This is snippy 4.6.0
[00:34:09] Written by Torsten Seemann
[00:34:09] Obtained from https://github.com/tseemann/snippy
[00:34:09] Detected operating system: linux
[00:34:09] Enabling bundled linux tools.
[00:34:09] Found bwa - /usr/local/bin/bwa
[00:34:09] Found bcftools - /usr/local/bin/bcftools
[00:34:09] Found samtools - /usr/local/bin/samtools
[00:34:09] Found java - /usr/local/bin/java
[00:34:09] Found snpEff - /usr/local/bin/snpEff
[00:34:09] Found samclip - /usr/local/bin/samclip
[00:34:09] Found seqtk - /usr/local/bin/seqtk
[00:34:09] Found parallel - /usr/local/bin/parallel
[00:34:09] Found freebayes - /usr/local/bin/freebayes
[00:34:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:34:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:34:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:34:09] Found vcfuniq - /usr/local/bin/vcfuniq
[00:34:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:34:09] Found gzip - /bin/gzip
[00:34:09] Found vt - /usr/local/bin/vt
[00:34:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:34:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:34:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:34:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:34:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:34:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:34:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:34:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:34:12] This is snippy 4.6.0Show full stderr[00:34:12] This is snippy 4.6.0
[00:34:12] Written by Torsten Seemann
[00:34:12] Obtained from https://github.com/tseemann/snippy
[00:34:12] Detected operating system: linux
[00:34:12] Enabling bundled linux tools.
[00:34:12] Found bwa - /usr/local/bin/bwa
[00:34:12] Found bcftools - /usr/local/bin/bcftools
[00:34:12] Found samtools - /usr/local/bin/samtools
[00:34:12] Found java - /usr/local/bin/java
[00:34:12] Found snpEff - /usr/local/bin/snpEff
[00:34:12] Found samclip - /usr/local/bin/samclip
[00:34:12] Found seqtk - /usr/local/bin/seqtk
[00:34:12] Found parallel - /usr/local/bin/parallel
[00:34:12] Found freebayes - /usr/local/bin/freebayes
[00:34:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:34:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:34:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:34:12] Found vcfuniq - /usr/local/bin/vcfuniq
[00:34:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:34:12] Found gzip - /bin/gzip
[00:34:12] Found vt - /usr/local/bin/vt
[00:34:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:34:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:34:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:34:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:34:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:34:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:34:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:34:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:53:44] This is snippy 4.6.0Show full stderr[00:53:44] This is snippy 4.6.0
[00:53:44] Written by Torsten Seemann
[00:53:44] Obtained from https://github.com/tseemann/snippy
[00:53:44] Detected operating system: linux
[00:53:44] Enabling bundled linux tools.
[00:53:44] Found bwa - /usr/local/bin/bwa
[00:53:44] Found bcftools - /usr/local/bin/bcftools
[00:53:44] Found samtools - /usr/local/bin/samtools
[00:53:44] Found java - /usr/local/bin/java
[00:53:44] Found snpEff - /usr/local/bin/snpEff
[00:53:44] Found samclip - /usr/local/bin/samclip
[00:53:44] Found seqtk - /usr/local/bin/seqtk
[00:53:44] Found parallel - /usr/local/bin/parallel
[00:53:44] Found freebayes - /usr/local/bin/freebayes
[00:53:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:53:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:53:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:53:44] Found vcfuniq - /usr/local/bin/vcfuniq
[00:53:44] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:53:44] Found gzip - /bin/gzip
[00:53:44] Found vt - /usr/local/bin/vt
[00:53:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:53:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:53:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:53:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:53:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:53:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:53:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:53:45] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:26:21] This is snippy 4.6.0Show full stderr[01:26:21] This is snippy 4.6.0
[01:26:21] Written by Torsten Seemann
[01:26:21] Obtained from https://github.com/tseemann/snippy
[01:26:21] Detected operating system: linux
[01:26:21] Enabling bundled linux tools.
[01:26:21] Found bwa - /usr/local/bin/bwa
[01:26:21] Found bcftools - /usr/local/bin/bcftools
[01:26:21] Found samtools - /usr/local/bin/samtools
[01:26:21] Found java - /usr/local/bin/java
[01:26:21] Found snpEff - /usr/local/bin/snpEff
[01:26:21] Found samclip - /usr/local/bin/samclip
[01:26:21] Found seqtk - /usr/local/bin/seqtk
[01:26:21] Found parallel - /usr/local/bin/parallel
[01:26:21] Found freebayes - /usr/local/bin/freebayes
[01:26:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:26:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:26:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:26:21] Found vcfuniq - /usr/local/bin/vcfuniq
[01:26:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:26:21] Found gzip - /bin/gzip
[01:26:21] Found vt - /usr/local/bin/vt
[01:26:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:26:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:26:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:26:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:26:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:26:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:26:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:26:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:29:37] This is snippy 4.6.0Show full stderr[01:29:37] This is snippy 4.6.0
[01:29:37] Written by Torsten Seemann
[01:29:37] Obtained from https://github.com/tseemann/snippy
[01:29:37] Detected operating system: linux
[01:29:37] Enabling bundled linux tools.
[01:29:37] Found bwa - /usr/local/bin/bwa
[01:29:37] Found bcftools - /usr/local/bin/bcftools
[01:29:37] Found samtools - /usr/local/bin/samtools
[01:29:37] Found java - /usr/local/bin/java
[01:29:37] Found snpEff - /usr/local/bin/snpEff
[01:29:37] Found samclip - /usr/local/bin/samclip
[01:29:37] Found seqtk - /usr/local/bin/seqtk
[01:29:37] Found parallel - /usr/local/bin/parallel
[01:29:37] Found freebayes - /usr/local/bin/freebayes
[01:29:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:29:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:29:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:29:37] Found vcfuniq - /usr/local/bin/vcfuniq
[01:29:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:29:37] Found gzip - /bin/gzip
[01:29:37] Found vt - /usr/local/bin/vt
[01:29:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:29:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:29:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:29:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:29:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:29:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:29:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:29:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:31:24] This is snippy 4.6.0Show full stderr[01:31:24] This is snippy 4.6.0
[01:31:24] Written by Torsten Seemann
[01:31:24] Obtained from https://github.com/tseemann/snippy
[01:31:24] Detected operating system: linux
[01:31:24] Enabling bundled linux tools.
[01:31:24] Found bwa - /usr/local/bin/bwa
[01:31:24] Found bcftools - /usr/local/bin/bcftools
[01:31:24] Found samtools - /usr/local/bin/samtools
[01:31:24] Found java - /usr/local/bin/java
[01:31:24] Found snpEff - /usr/local/bin/snpEff
[01:31:24] Found samclip - /usr/local/bin/samclip
[01:31:24] Found seqtk - /usr/local/bin/seqtk
[01:31:24] Found parallel - /usr/local/bin/parallel
[01:31:24] Found freebayes - /usr/local/bin/freebayes
[01:31:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:31:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:31:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:31:24] Found vcfuniq - /usr/local/bin/vcfuniq
[01:31:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:31:24] Found gzip - /bin/gzip
[01:31:24] Found vt - /usr/local/bin/vt
[01:31:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:31:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:31:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:31:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:31:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:31:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:31:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:31:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:31:39] This is snippy 4.6.0Show full stderr[01:31:39] This is snippy 4.6.0
[01:31:39] Written by Torsten Seemann
[01:31:39] Obtained from https://github.com/tseemann/snippy
[01:31:39] Detected operating system: linux
[01:31:39] Enabling bundled linux tools.
[01:31:39] Found bwa - /usr/local/bin/bwa
[01:31:39] Found bcftools - /usr/local/bin/bcftools
[01:31:39] Found samtools - /usr/local/bin/samtools
[01:31:39] Found java - /usr/local/bin/java
[01:31:39] Found snpEff - /usr/local/bin/snpEff
[01:31:39] Found samclip - /usr/local/bin/samclip
[01:31:39] Found seqtk - /usr/local/bin/seqtk
[01:31:39] Found parallel - /usr/local/bin/parallel
[01:31:39] Found freebayes - /usr/local/bin/freebayes
[01:31:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:31:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:31:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:31:39] Found vcfuniq - /usr/local/bin/vcfuniq
[01:31:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:31:39] Found gzip - /bin/gzip
[01:31:39] Found vt - /usr/local/bin/vt
[01:31:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:31:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:31:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:31:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:31:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:31:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:31:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:31:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:34:19] This is snippy 4.6.0Show full stderr[01:34:19] This is snippy 4.6.0
[01:34:19] Written by Torsten Seemann
[01:34:19] Obtained from https://github.com/tseemann/snippy
[01:34:19] Detected operating system: linux
[01:34:19] Enabling bundled linux tools.
[01:34:19] Found bwa - /usr/local/bin/bwa
[01:34:19] Found bcftools - /usr/local/bin/bcftools
[01:34:19] Found samtools - /usr/local/bin/samtools
[01:34:19] Found java - /usr/local/bin/java
[01:34:19] Found snpEff - /usr/local/bin/snpEff
[01:34:19] Found samclip - /usr/local/bin/samclip
[01:34:19] Found seqtk - /usr/local/bin/seqtk
[01:34:19] Found parallel - /usr/local/bin/parallel
[01:34:19] Found freebayes - /usr/local/bin/freebayes
[01:34:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:34:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:34:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:34:19] Found vcfuniq - /usr/local/bin/vcfuniq
[01:34:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:34:19] Found gzip - /bin/gzip
[01:34:19] Found vt - /usr/local/bin/vt
[01:34:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:34:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:34:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:34:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:34:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:34:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:34:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:34:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:36:34] This is snippy 4.6.0Show full stderr[01:36:34] This is snippy 4.6.0
[01:36:34] Written by Torsten Seemann
[01:36:34] Obtained from https://github.com/tseemann/snippy
[01:36:34] Detected operating system: linux
[01:36:34] Enabling bundled linux tools.
[01:36:34] Found bwa - /usr/local/bin/bwa
[01:36:34] Found bcftools - /usr/local/bin/bcftools
[01:36:34] Found samtools - /usr/local/bin/samtools
[01:36:34] Found java - /usr/local/bin/java
[01:36:34] Found snpEff - /usr/local/bin/snpEff
[01:36:34] Found samclip - /usr/local/bin/samclip
[01:36:34] Found seqtk - /usr/local/bin/seqtk
[01:36:35] Found parallel - /usr/local/bin/parallel
[01:36:35] Found freebayes - /usr/local/bin/freebayes
[01:36:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:36:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:36:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:36:35] Found vcfuniq - /usr/local/bin/vcfuniq
[01:36:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:36:35] Found gzip - /bin/gzip
[01:36:35] Found vt - /usr/local/bin/vt
[01:36:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:36:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:36:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:36:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:36:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:36:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:36:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:36:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:50:07] This is snippy 4.6.0Show full stderr[01:50:07] This is snippy 4.6.0
[01:50:07] Written by Torsten Seemann
[01:50:07] Obtained from https://github.com/tseemann/snippy
[01:50:07] Detected operating system: linux
[01:50:07] Enabling bundled linux tools.
[01:50:07] Found bwa - /usr/local/bin/bwa
[01:50:07] Found bcftools - /usr/local/bin/bcftools
[01:50:07] Found samtools - /usr/local/bin/samtools
[01:50:07] Found java - /usr/local/bin/java
[01:50:07] Found snpEff - /usr/local/bin/snpEff
[01:50:07] Found samclip - /usr/local/bin/samclip
[01:50:07] Found seqtk - /usr/local/bin/seqtk
[01:50:07] Found parallel - /usr/local/bin/parallel
[01:50:07] Found freebayes - /usr/local/bin/freebayes
[01:50:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:50:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:50:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:50:07] Found vcfuniq - /usr/local/bin/vcfuniq
[01:50:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:50:07] Found gzip - /bin/gzip
[01:50:07] Found vt - /usr/local/bin/vt
[01:50:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:50:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:50:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:50:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:50:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:50:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:50:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:50:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:57:58] This is snippy 4.6.0Show full stderr[01:57:58] This is snippy 4.6.0
[01:57:58] Written by Torsten Seemann
[01:57:58] Obtained from https://github.com/tseemann/snippy
[01:57:58] Detected operating system: linux
[01:57:58] Enabling bundled linux tools.
[01:57:58] Found bwa - /usr/local/bin/bwa
[01:57:58] Found bcftools - /usr/local/bin/bcftools
[01:57:58] Found samtools - /usr/local/bin/samtools
[01:57:58] Found java - /usr/local/bin/java
[01:57:58] Found snpEff - /usr/local/bin/snpEff
[01:57:58] Found samclip - /usr/local/bin/samclip
[01:57:58] Found seqtk - /usr/local/bin/seqtk
[01:57:58] Found parallel - /usr/local/bin/parallel
[01:57:58] Found freebayes - /usr/local/bin/freebayes
[01:57:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:57:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:57:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:57:58] Found vcfuniq - /usr/local/bin/vcfuniq
[01:57:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:57:58] Found gzip - /bin/gzip
[01:57:58] Found vt - /usr/local/bin/vt
[01:57:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:57:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:57:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:57:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:57:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:58:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:58:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:58:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:45:38] This is snippy 4.6.0Show full stderr[01:45:38] This is snippy 4.6.0
[01:45:38] Written by Torsten Seemann
[01:45:38] Obtained from https://github.com/tseemann/snippy
[01:45:38] Detected operating system: linux
[01:45:38] Enabling bundled linux tools.
[01:45:38] Found bwa - /usr/local/bin/bwa
[01:45:38] Found bcftools - /usr/local/bin/bcftools
[01:45:38] Found samtools - /usr/local/bin/samtools
[01:45:38] Found java - /usr/local/bin/java
[01:45:38] Found snpEff - /usr/local/bin/snpEff
[01:45:38] Found samclip - /usr/local/bin/samclip
[01:45:38] Found seqtk - /usr/local/bin/seqtk
[01:45:38] Found parallel - /usr/local/bin/parallel
[01:45:38] Found freebayes - /usr/local/bin/freebayes
[01:45:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:45:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:45:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:45:38] Found vcfuniq - /usr/local/bin/vcfuniq
[01:45:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:45:38] Found gzip - /bin/gzip
[01:45:38] Found vt - /usr/local/bin/vt
[01:45:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:45:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:45:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:45:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:45:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:45:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:45:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:45:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:46:15] This is snippy 4.6.0Show full stderr[01:46:15] This is snippy 4.6.0
[01:46:15] Written by Torsten Seemann
[01:46:15] Obtained from https://github.com/tseemann/snippy
[01:46:15] Detected operating system: linux
[01:46:15] Enabling bundled linux tools.
[01:46:15] Found bwa - /usr/local/bin/bwa
[01:46:15] Found bcftools - /usr/local/bin/bcftools
[01:46:15] Found samtools - /usr/local/bin/samtools
[01:46:15] Found java - /usr/local/bin/java
[01:46:15] Found snpEff - /usr/local/bin/snpEff
[01:46:15] Found samclip - /usr/local/bin/samclip
[01:46:15] Found seqtk - /usr/local/bin/seqtk
[01:46:15] Found parallel - /usr/local/bin/parallel
[01:46:15] Found freebayes - /usr/local/bin/freebayes
[01:46:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:46:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:46:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:46:15] Found vcfuniq - /usr/local/bin/vcfuniq
[01:46:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:46:15] Found gzip - /bin/gzip
[01:46:15] Found vt - /usr/local/bin/vt
[01:46:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:46:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:46:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:46:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:46:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:46:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:46:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:46:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:46:30] This is snippy 4.6.0Show full stderr[01:46:30] This is snippy 4.6.0
[01:46:30] Written by Torsten Seemann
[01:46:30] Obtained from https://github.com/tseemann/snippy
[01:46:30] Detected operating system: linux
[01:46:30] Enabling bundled linux tools.
[01:46:30] Found bwa - /usr/local/bin/bwa
[01:46:30] Found bcftools - /usr/local/bin/bcftools
[01:46:30] Found samtools - /usr/local/bin/samtools
[01:46:30] Found java - /usr/local/bin/java
[01:46:30] Found snpEff - /usr/local/bin/snpEff
[01:46:30] Found samclip - /usr/local/bin/samclip
[01:46:30] Found seqtk - /usr/local/bin/seqtk
[01:46:30] Found parallel - /usr/local/bin/parallel
[01:46:30] Found freebayes - /usr/local/bin/freebayes
[01:46:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:46:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:46:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:46:30] Found vcfuniq - /usr/local/bin/vcfuniq
[01:46:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:46:30] Found gzip - /bin/gzip
[01:46:30] Found vt - /usr/local/bin/vt
[01:46:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:46:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:46:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:46:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:46:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:46:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:46:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:46:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:47:42] This is snippy 4.6.0Show full stderr[01:47:42] This is snippy 4.6.0
[01:47:42] Written by Torsten Seemann
[01:47:42] Obtained from https://github.com/tseemann/snippy
[01:47:42] Detected operating system: linux
[01:47:42] Enabling bundled linux tools.
[01:47:42] Found bwa - /usr/local/bin/bwa
[01:47:42] Found bcftools - /usr/local/bin/bcftools
[01:47:42] Found samtools - /usr/local/bin/samtools
[01:47:42] Found java - /usr/local/bin/java
[01:47:42] Found snpEff - /usr/local/bin/snpEff
[01:47:42] Found samclip - /usr/local/bin/samclip
[01:47:42] Found seqtk - /usr/local/bin/seqtk
[01:47:42] Found parallel - /usr/local/bin/parallel
[01:47:42] Found freebayes - /usr/local/bin/freebayes
[01:47:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:47:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:47:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:47:42] Found vcfuniq - /usr/local/bin/vcfuniq
[01:47:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:47:42] Found gzip - /bin/gzip
[01:47:42] Found vt - /usr/local/bin/vt
[01:47:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:47:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:47:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:47:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:47:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:47:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:47:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:47:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:47:54] This is snippy 4.6.0Show full stderr[01:47:54] This is snippy 4.6.0
[01:47:54] Written by Torsten Seemann
[01:47:54] Obtained from https://github.com/tseemann/snippy
[01:47:54] Detected operating system: linux
[01:47:54] Enabling bundled linux tools.
[01:47:54] Found bwa - /usr/local/bin/bwa
[01:47:54] Found bcftools - /usr/local/bin/bcftools
[01:47:54] Found samtools - /usr/local/bin/samtools
[01:47:54] Found java - /usr/local/bin/java
[01:47:54] Found snpEff - /usr/local/bin/snpEff
[01:47:54] Found samclip - /usr/local/bin/samclip
[01:47:54] Found seqtk - /usr/local/bin/seqtk
[01:47:54] Found parallel - /usr/local/bin/parallel
[01:47:54] Found freebayes - /usr/local/bin/freebayes
[01:47:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:47:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:47:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:47:54] Found vcfuniq - /usr/local/bin/vcfuniq
[01:47:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:47:54] Found gzip - /bin/gzip
[01:47:54] Found vt - /usr/local/bin/vt
[01:47:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:47:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:47:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:47:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:47:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:47:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:47:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:47:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:59:41] This is snippy 4.6.0Show full stderr[01:59:41] This is snippy 4.6.0
[01:59:41] Written by Torsten Seemann
[01:59:41] Obtained from https://github.com/tseemann/snippy
[01:59:41] Detected operating system: linux
[01:59:41] Enabling bundled linux tools.
[01:59:41] Found bwa - /usr/local/bin/bwa
[01:59:42] Found bcftools - /usr/local/bin/bcftools
[01:59:42] Found samtools - /usr/local/bin/samtools
[01:59:42] Found java - /usr/local/bin/java
[01:59:42] Found snpEff - /usr/local/bin/snpEff
[01:59:42] Found samclip - /usr/local/bin/samclip
[01:59:42] Found seqtk - /usr/local/bin/seqtk
[01:59:42] Found parallel - /usr/local/bin/parallel
[01:59:42] Found freebayes - /usr/local/bin/freebayes
[01:59:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:59:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:59:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:59:42] Found vcfuniq - /usr/local/bin/vcfuniq
[01:59:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:59:42] Found gzip - /bin/gzip
[01:59:42] Found vt - /usr/local/bin/vt
[01:59:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:59:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:59:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:59:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:59:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:59:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:59:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:59:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:10:16] This is snippy 4.6.0Show full stderr[01:10:16] This is snippy 4.6.0
[01:10:16] Written by Torsten Seemann
[01:10:16] Obtained from https://github.com/tseemann/snippy
[01:10:16] Detected operating system: linux
[01:10:16] Enabling bundled linux tools.
[01:10:16] Found bwa - /usr/local/bin/bwa
[01:10:16] Found bcftools - /usr/local/bin/bcftools
[01:10:16] Found samtools - /usr/local/bin/samtools
[01:10:16] Found java - /usr/local/bin/java
[01:10:16] Found snpEff - /usr/local/bin/snpEff
[01:10:17] Found samclip - /usr/local/bin/samclip
[01:10:17] Found seqtk - /usr/local/bin/seqtk
[01:10:17] Found parallel - /usr/local/bin/parallel
[01:10:17] Found freebayes - /usr/local/bin/freebayes
[01:10:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:10:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:10:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:10:17] Found vcfuniq - /usr/local/bin/vcfuniq
[01:10:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:10:17] Found gzip - /bin/gzip
[01:10:17] Found vt - /usr/local/bin/vt
[01:10:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:10:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:10:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:10:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:10:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:10:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:10:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:10:18] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:10:31] This is snippy 4.6.0Show full stderr[01:10:31] This is snippy 4.6.0
[01:10:31] Written by Torsten Seemann
[01:10:31] Obtained from https://github.com/tseemann/snippy
[01:10:31] Detected operating system: linux
[01:10:31] Enabling bundled linux tools.
[01:10:31] Found bwa - /usr/local/bin/bwa
[01:10:31] Found bcftools - /usr/local/bin/bcftools
[01:10:31] Found samtools - /usr/local/bin/samtools
[01:10:31] Found java - /usr/local/bin/java
[01:10:31] Found snpEff - /usr/local/bin/snpEff
[01:10:31] Found samclip - /usr/local/bin/samclip
[01:10:31] Found seqtk - /usr/local/bin/seqtk
[01:10:31] Found parallel - /usr/local/bin/parallel
[01:10:31] Found freebayes - /usr/local/bin/freebayes
[01:10:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:10:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:10:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:10:32] Found vcfuniq - /usr/local/bin/vcfuniq
[01:10:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:10:32] Found gzip - /bin/gzip
[01:10:32] Found vt - /usr/local/bin/vt
[01:10:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:10:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:10:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:10:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:10:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:10:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:10:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:10:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:13:13] This is snippy 4.6.0Show full stderr[01:13:13] This is snippy 4.6.0
[01:13:13] Written by Torsten Seemann
[01:13:13] Obtained from https://github.com/tseemann/snippy
[01:13:13] Detected operating system: linux
[01:13:13] Enabling bundled linux tools.
[01:13:13] Found bwa - /usr/local/bin/bwa
[01:13:13] Found bcftools - /usr/local/bin/bcftools
[01:13:13] Found samtools - /usr/local/bin/samtools
[01:13:13] Found java - /usr/local/bin/java
[01:13:13] Found snpEff - /usr/local/bin/snpEff
[01:13:13] Found samclip - /usr/local/bin/samclip
[01:13:13] Found seqtk - /usr/local/bin/seqtk
[01:13:13] Found parallel - /usr/local/bin/parallel
[01:13:13] Found freebayes - /usr/local/bin/freebayes
[01:13:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:13:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:13:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:13:13] Found vcfuniq - /usr/local/bin/vcfuniq
[01:13:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:13:13] Found gzip - /bin/gzip
[01:13:13] Found vt - /usr/local/bin/vt
[01:13:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:13:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:13:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:13:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:13:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:13:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:13:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:13:14] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:46:10] This is snippy 4.6.0Show full stderr[01:46:10] This is snippy 4.6.0
[01:46:10] Written by Torsten Seemann
[01:46:10] Obtained from https://github.com/tseemann/snippy
[01:46:10] Detected operating system: linux
[01:46:10] Enabling bundled linux tools.
[01:46:10] Found bwa - /usr/local/bin/bwa
[01:46:10] Found bcftools - /usr/local/bin/bcftools
[01:46:10] Found samtools - /usr/local/bin/samtools
[01:46:10] Found java - /usr/local/bin/java
[01:46:10] Found snpEff - /usr/local/bin/snpEff
[01:46:10] Found samclip - /usr/local/bin/samclip
[01:46:10] Found seqtk - /usr/local/bin/seqtk
[01:46:10] Found parallel - /usr/local/bin/parallel
[01:46:10] Found freebayes - /usr/local/bin/freebayes
[01:46:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:46:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:46:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:46:10] Found vcfuniq - /usr/local/bin/vcfuniq
[01:46:10] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:46:10] Found gzip - /bin/gzip
[01:46:10] Found vt - /usr/local/bin/vt
[01:46:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:46:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:46:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:46:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:46:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:46:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:46:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:46:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:13:57] This is snippy 4.6.0Show full stderr[01:13:57] This is snippy 4.6.0
[01:13:57] Written by Torsten Seemann
[01:13:57] Obtained from https://github.com/tseemann/snippy
[01:13:57] Detected operating system: linux
[01:13:57] Enabling bundled linux tools.
[01:13:57] Found bwa - /usr/local/bin/bwa
[01:13:57] Found bcftools - /usr/local/bin/bcftools
[01:13:57] Found samtools - /usr/local/bin/samtools
[01:13:57] Found java - /usr/local/bin/java
[01:13:57] Found snpEff - /usr/local/bin/snpEff
[01:13:57] Found samclip - /usr/local/bin/samclip
[01:13:57] Found seqtk - /usr/local/bin/seqtk
[01:13:57] Found parallel - /usr/local/bin/parallel
[01:13:57] Found freebayes - /usr/local/bin/freebayes
[01:13:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:13:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:13:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:13:57] Found vcfuniq - /usr/local/bin/vcfuniq
[01:13:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:13:57] Found gzip - /bin/gzip
[01:13:57] Found vt - /usr/local/bin/vt
[01:13:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:13:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:13:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:13:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:13:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:13:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:13:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:13:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:47:39] This is snippy 4.6.0Show full stderr[01:47:39] This is snippy 4.6.0
[01:47:39] Written by Torsten Seemann
[01:47:39] Obtained from https://github.com/tseemann/snippy
[01:47:39] Detected operating system: linux
[01:47:39] Enabling bundled linux tools.
[01:47:39] Found bwa - /usr/local/bin/bwa
[01:47:39] Found bcftools - /usr/local/bin/bcftools
[01:47:39] Found samtools - /usr/local/bin/samtools
[01:47:39] Found java - /usr/local/bin/java
[01:47:39] Found snpEff - /usr/local/bin/snpEff
[01:47:39] Found samclip - /usr/local/bin/samclip
[01:47:39] Found seqtk - /usr/local/bin/seqtk
[01:47:39] Found parallel - /usr/local/bin/parallel
[01:47:39] Found freebayes - /usr/local/bin/freebayes
[01:47:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:47:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:47:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:47:39] Found vcfuniq - /usr/local/bin/vcfuniq
[01:47:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:47:39] Found gzip - /bin/gzip
[01:47:39] Found vt - /usr/local/bin/vt
[01:47:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:47:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:47:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:47:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:47:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:47:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:47:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:47:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:14:12] This is snippy 4.6.0Show full stderr[01:14:12] This is snippy 4.6.0
[01:14:12] Written by Torsten Seemann
[01:14:12] Obtained from https://github.com/tseemann/snippy
[01:14:12] Detected operating system: linux
[01:14:12] Enabling bundled linux tools.
[01:14:12] Found bwa - /usr/local/bin/bwa
[01:14:12] Found bcftools - /usr/local/bin/bcftools
[01:14:12] Found samtools - /usr/local/bin/samtools
[01:14:12] Found java - /usr/local/bin/java
[01:14:12] Found snpEff - /usr/local/bin/snpEff
[01:14:12] Found samclip - /usr/local/bin/samclip
[01:14:12] Found seqtk - /usr/local/bin/seqtk
[01:14:12] Found parallel - /usr/local/bin/parallel
[01:14:12] Found freebayes - /usr/local/bin/freebayes
[01:14:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:14:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:14:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:14:12] Found vcfuniq - /usr/local/bin/vcfuniq
[01:14:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:14:12] Found gzip - /bin/gzip
[01:14:12] Found vt - /usr/local/bin/vt
[01:14:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:14:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:14:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:14:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:14:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:14:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:14:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:14:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:14:30] This is snippy 4.6.0Show full stderr[01:14:30] This is snippy 4.6.0
[01:14:30] Written by Torsten Seemann
[01:14:30] Obtained from https://github.com/tseemann/snippy
[01:14:30] Detected operating system: linux
[01:14:30] Enabling bundled linux tools.
[01:14:30] Found bwa - /usr/local/bin/bwa
[01:14:30] Found bcftools - /usr/local/bin/bcftools
[01:14:30] Found samtools - /usr/local/bin/samtools
[01:14:30] Found java - /usr/local/bin/java
[01:14:30] Found snpEff - /usr/local/bin/snpEff
[01:14:30] Found samclip - /usr/local/bin/samclip
[01:14:30] Found seqtk - /usr/local/bin/seqtk
[01:14:30] Found parallel - /usr/local/bin/parallel
[01:14:30] Found freebayes - /usr/local/bin/freebayes
[01:14:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:14:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:14:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:14:30] Found vcfuniq - /usr/local/bin/vcfuniq
[01:14:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:14:30] Found gzip - /bin/gzip
[01:14:30] Found vt - /usr/local/bin/vt
[01:14:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:14:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:14:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:14:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:14:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:14:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:14:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:14:31] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:15:24] This is snippy 4.6.0Show full stderr[01:15:24] This is snippy 4.6.0
[01:15:24] Written by Torsten Seemann
[01:15:24] Obtained from https://github.com/tseemann/snippy
[01:15:24] Detected operating system: linux
[01:15:24] Enabling bundled linux tools.
[01:15:24] Found bwa - /usr/local/bin/bwa
[01:15:24] Found bcftools - /usr/local/bin/bcftools
[01:15:24] Found samtools - /usr/local/bin/samtools
[01:15:24] Found java - /usr/local/bin/java
[01:15:24] Found snpEff - /usr/local/bin/snpEff
[01:15:24] Found samclip - /usr/local/bin/samclip
[01:15:24] Found seqtk - /usr/local/bin/seqtk
[01:15:24] Found parallel - /usr/local/bin/parallel
[01:15:24] Found freebayes - /usr/local/bin/freebayes
[01:15:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:15:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:15:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:15:24] Found vcfuniq - /usr/local/bin/vcfuniq
[01:15:24] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:15:24] Found gzip - /bin/gzip
[01:15:24] Found vt - /usr/local/bin/vt
[01:15:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:15:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:15:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:15:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:15:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:15:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:15:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:15:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:51:24] This is snippy 4.6.0Show full stderr[01:51:24] This is snippy 4.6.0
[01:51:24] Written by Torsten Seemann
[01:51:24] Obtained from https://github.com/tseemann/snippy
[01:51:24] Detected operating system: linux
[01:51:24] Enabling bundled linux tools.
[01:51:24] Found bwa - /usr/local/bin/bwa
[01:51:24] Found bcftools - /usr/local/bin/bcftools
[01:51:24] Found samtools - /usr/local/bin/samtools
[01:51:24] Found java - /usr/local/bin/java
[01:51:24] Found snpEff - /usr/local/bin/snpEff
[01:51:24] Found samclip - /usr/local/bin/samclip
[01:51:24] Found seqtk - /usr/local/bin/seqtk
[01:51:24] Found parallel - /usr/local/bin/parallel
[01:51:25] Found freebayes - /usr/local/bin/freebayes
[01:51:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:51:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:51:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:51:25] Found vcfuniq - /usr/local/bin/vcfuniq
[01:51:25] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:51:25] Found gzip - /bin/gzip
[01:51:25] Found vt - /usr/local/bin/vt
[01:51:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:51:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:51:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:51:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:51:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:51:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:51:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:51:25] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:20:30] This is snippy 4.6.0Show full stderr[01:20:30] This is snippy 4.6.0
[01:20:30] Written by Torsten Seemann
[01:20:30] Obtained from https://github.com/tseemann/snippy
[01:20:30] Detected operating system: linux
[01:20:30] Enabling bundled linux tools.
[01:20:30] Found bwa - /usr/local/bin/bwa
[01:20:30] Found bcftools - /usr/local/bin/bcftools
[01:20:30] Found samtools - /usr/local/bin/samtools
[01:20:30] Found java - /usr/local/bin/java
[01:20:30] Found snpEff - /usr/local/bin/snpEff
[01:20:30] Found samclip - /usr/local/bin/samclip
[01:20:30] Found seqtk - /usr/local/bin/seqtk
[01:20:30] Found parallel - /usr/local/bin/parallel
[01:20:30] Found freebayes - /usr/local/bin/freebayes
[01:20:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:20:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:20:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:20:30] Found vcfuniq - /usr/local/bin/vcfuniq
[01:20:30] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:20:30] Found gzip - /bin/gzip
[01:20:30] Found vt - /usr/local/bin/vt
[01:20:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:20:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:20:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:20:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:20:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:20:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:20:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:20:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:21:02] This is snippy 4.6.0Show full stderr[01:21:02] This is snippy 4.6.0
[01:21:02] Written by Torsten Seemann
[01:21:02] Obtained from https://github.com/tseemann/snippy
[01:21:02] Detected operating system: linux
[01:21:02] Enabling bundled linux tools.
[01:21:02] Found bwa - /usr/local/bin/bwa
[01:21:02] Found bcftools - /usr/local/bin/bcftools
[01:21:02] Found samtools - /usr/local/bin/samtools
[01:21:02] Found java - /usr/local/bin/java
[01:21:02] Found snpEff - /usr/local/bin/snpEff
[01:21:02] Found samclip - /usr/local/bin/samclip
[01:21:02] Found seqtk - /usr/local/bin/seqtk
[01:21:02] Found parallel - /usr/local/bin/parallel
[01:21:02] Found freebayes - /usr/local/bin/freebayes
[01:21:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:21:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:21:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:21:02] Found vcfuniq - /usr/local/bin/vcfuniq
[01:21:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:21:02] Found gzip - /bin/gzip
[01:21:02] Found vt - /usr/local/bin/vt
[01:21:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:21:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:21:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:21:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:21:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:21:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:21:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:21:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:23:28] This is snippy 4.6.0Show full stderr[01:23:28] This is snippy 4.6.0
[01:23:28] Written by Torsten Seemann
[01:23:28] Obtained from https://github.com/tseemann/snippy
[01:23:28] Detected operating system: linux
[01:23:28] Enabling bundled linux tools.
[01:23:28] Found bwa - /usr/local/bin/bwa
[01:23:28] Found bcftools - /usr/local/bin/bcftools
[01:23:28] Found samtools - /usr/local/bin/samtools
[01:23:28] Found java - /usr/local/bin/java
[01:23:28] Found snpEff - /usr/local/bin/snpEff
[01:23:28] Found samclip - /usr/local/bin/samclip
[01:23:28] Found seqtk - /usr/local/bin/seqtk
[01:23:28] Found parallel - /usr/local/bin/parallel
[01:23:28] Found freebayes - /usr/local/bin/freebayes
[01:23:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:23:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:23:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:23:28] Found vcfuniq - /usr/local/bin/vcfuniq
[01:23:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:23:28] Found gzip - /bin/gzip
[01:23:28] Found vt - /usr/local/bin/vt
[01:23:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:23:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:23:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:23:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:23:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:23:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:23:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:23:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:52:53] This is snippy 4.6.0Show full stderr[01:52:53] This is snippy 4.6.0
[01:52:53] Written by Torsten Seemann
[01:52:53] Obtained from https://github.com/tseemann/snippy
[01:52:53] Detected operating system: linux
[01:52:53] Enabling bundled linux tools.
[01:52:53] Found bwa - /usr/local/bin/bwa
[01:52:53] Found bcftools - /usr/local/bin/bcftools
[01:52:53] Found samtools - /usr/local/bin/samtools
[01:52:53] Found java - /usr/local/bin/java
[01:52:53] Found snpEff - /usr/local/bin/snpEff
[01:52:53] Found samclip - /usr/local/bin/samclip
[01:52:53] Found seqtk - /usr/local/bin/seqtk
[01:52:53] Found parallel - /usr/local/bin/parallel
[01:52:53] Found freebayes - /usr/local/bin/freebayes
[01:52:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:52:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:52:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:52:53] Found vcfuniq - /usr/local/bin/vcfuniq
[01:52:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:52:53] Found gzip - /bin/gzip
[01:52:53] Found vt - /usr/local/bin/vt
[01:52:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:52:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:52:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:52:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:52:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:52:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:52:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:52:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:23:51] This is snippy 4.6.0Show full stderr[01:23:51] This is snippy 4.6.0
[01:23:51] Written by Torsten Seemann
[01:23:51] Obtained from https://github.com/tseemann/snippy
[01:23:51] Detected operating system: linux
[01:23:51] Enabling bundled linux tools.
[01:23:51] Found bwa - /usr/local/bin/bwa
[01:23:51] Found bcftools - /usr/local/bin/bcftools
[01:23:51] Found samtools - /usr/local/bin/samtools
[01:23:51] Found java - /usr/local/bin/java
[01:23:51] Found snpEff - /usr/local/bin/snpEff
[01:23:51] Found samclip - /usr/local/bin/samclip
[01:23:51] Found seqtk - /usr/local/bin/seqtk
[01:23:51] Found parallel - /usr/local/bin/parallel
[01:23:51] Found freebayes - /usr/local/bin/freebayes
[01:23:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:23:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:23:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:23:51] Found vcfuniq - /usr/local/bin/vcfuniq
[01:23:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:23:52] Found gzip - /bin/gzip
[01:23:52] Found vt - /usr/local/bin/vt
[01:23:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:23:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:23:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:23:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:23:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:23:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:23:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:23:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:09] This is snippy 4.6.0Show full stderr[00:31:09] This is snippy 4.6.0
[00:31:09] Written by Torsten Seemann
[00:31:09] Obtained from https://github.com/tseemann/snippy
[00:31:09] Detected operating system: linux
[00:31:09] Enabling bundled linux tools.
[00:31:09] Found bwa - /usr/local/bin/bwa
[00:31:09] Found bcftools - /usr/local/bin/bcftools
[00:31:09] Found samtools - /usr/local/bin/samtools
[00:31:09] Found java - /usr/local/bin/java
[00:31:09] Found snpEff - /usr/local/bin/snpEff
[00:31:09] Found samclip - /usr/local/bin/samclip
[00:31:09] Found seqtk - /usr/local/bin/seqtk
[00:31:09] Found parallel - /usr/local/bin/parallel
[00:31:09] Found freebayes - /usr/local/bin/freebayes
[00:31:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:09] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:09] Found gzip - /bin/gzip
[00:31:09] Found vt - /usr/local/bin/vt
[00:31:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:48] This is snippy 4.6.0Show full stderr[00:31:48] This is snippy 4.6.0
[00:31:48] Written by Torsten Seemann
[00:31:48] Obtained from https://github.com/tseemann/snippy
[00:31:48] Detected operating system: linux
[00:31:48] Enabling bundled linux tools.
[00:31:48] Found bwa - /usr/local/bin/bwa
[00:31:48] Found bcftools - /usr/local/bin/bcftools
[00:31:48] Found samtools - /usr/local/bin/samtools
[00:31:48] Found java - /usr/local/bin/java
[00:31:48] Found snpEff - /usr/local/bin/snpEff
[00:31:48] Found samclip - /usr/local/bin/samclip
[00:31:48] Found seqtk - /usr/local/bin/seqtk
[00:31:48] Found parallel - /usr/local/bin/parallel
[00:31:48] Found freebayes - /usr/local/bin/freebayes
[00:31:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:48] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:48] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:48] Found gzip - /bin/gzip
[00:31:48] Found vt - /usr/local/bin/vt
[00:31:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:49] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:41:26] This is snippy 4.6.0Show full stderr[00:41:26] This is snippy 4.6.0
[00:41:26] Written by Torsten Seemann
[00:41:26] Obtained from https://github.com/tseemann/snippy
[00:41:26] Detected operating system: linux
[00:41:26] Enabling bundled linux tools.
[00:41:26] Found bwa - /usr/local/bin/bwa
[00:41:26] Found bcftools - /usr/local/bin/bcftools
[00:41:26] Found samtools - /usr/local/bin/samtools
[00:41:26] Found java - /usr/local/bin/java
[00:41:26] Found snpEff - /usr/local/bin/snpEff
[00:41:26] Found samclip - /usr/local/bin/samclip
[00:41:26] Found seqtk - /usr/local/bin/seqtk
[00:41:26] Found parallel - /usr/local/bin/parallel
[00:41:26] Found freebayes - /usr/local/bin/freebayes
[00:41:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:41:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:41:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:41:26] Found vcfuniq - /usr/local/bin/vcfuniq
[00:41:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:41:26] Found gzip - /bin/gzip
[00:41:26] Found vt - /usr/local/bin/vt
[00:41:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:41:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:41:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:41:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:41:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:41:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:41:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:41:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:31:58] This is snippy 4.6.0Show full stderr[00:31:58] This is snippy 4.6.0
[00:31:58] Written by Torsten Seemann
[00:31:58] Obtained from https://github.com/tseemann/snippy
[00:31:58] Detected operating system: linux
[00:31:58] Enabling bundled linux tools.
[00:31:58] Found bwa - /usr/local/bin/bwa
[00:31:58] Found bcftools - /usr/local/bin/bcftools
[00:31:58] Found samtools - /usr/local/bin/samtools
[00:31:58] Found java - /usr/local/bin/java
[00:31:58] Found snpEff - /usr/local/bin/snpEff
[00:31:58] Found samclip - /usr/local/bin/samclip
[00:31:58] Found seqtk - /usr/local/bin/seqtk
[00:31:58] Found parallel - /usr/local/bin/parallel
[00:31:58] Found freebayes - /usr/local/bin/freebayes
[00:31:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:31:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:31:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:31:58] Found vcfuniq - /usr/local/bin/vcfuniq
[00:31:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:31:58] Found gzip - /bin/gzip
[00:31:58] Found vt - /usr/local/bin/vt
[00:31:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:31:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:31:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:31:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:31:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:31:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:31:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:31:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:41:39] This is snippy 4.6.0Show full stderr[00:41:39] This is snippy 4.6.0
[00:41:39] Written by Torsten Seemann
[00:41:39] Obtained from https://github.com/tseemann/snippy
[00:41:39] Detected operating system: linux
[00:41:39] Enabling bundled linux tools.
[00:41:39] Found bwa - /usr/local/bin/bwa
[00:41:39] Found bcftools - /usr/local/bin/bcftools
[00:41:39] Found samtools - /usr/local/bin/samtools
[00:41:39] Found java - /usr/local/bin/java
[00:41:39] Found snpEff - /usr/local/bin/snpEff
[00:41:39] Found samclip - /usr/local/bin/samclip
[00:41:39] Found seqtk - /usr/local/bin/seqtk
[00:41:39] Found parallel - /usr/local/bin/parallel
[00:41:39] Found freebayes - /usr/local/bin/freebayes
[00:41:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:41:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:41:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:41:39] Found vcfuniq - /usr/local/bin/vcfuniq
[00:41:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:41:39] Found gzip - /bin/gzip
[00:41:39] Found vt - /usr/local/bin/vt
[00:41:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:41:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:41:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:41:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:41:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:41:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:41:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:41:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:32:01] This is snippy 4.6.0Show full stderr[00:32:01] This is snippy 4.6.0
[00:32:01] Written by Torsten Seemann
[00:32:01] Obtained from https://github.com/tseemann/snippy
[00:32:01] Detected operating system: linux
[00:32:01] Enabling bundled linux tools.
[00:32:01] Found bwa - /usr/local/bin/bwa
[00:32:01] Found bcftools - /usr/local/bin/bcftools
[00:32:01] Found samtools - /usr/local/bin/samtools
[00:32:01] Found java - /usr/local/bin/java
[00:32:01] Found snpEff - /usr/local/bin/snpEff
[00:32:01] Found samclip - /usr/local/bin/samclip
[00:32:01] Found seqtk - /usr/local/bin/seqtk
[00:32:01] Found parallel - /usr/local/bin/parallel
[00:32:01] Found freebayes - /usr/local/bin/freebayes
[00:32:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:32:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:32:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:32:01] Found vcfuniq - /usr/local/bin/vcfuniq
[00:32:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:32:01] Found gzip - /bin/gzip
[00:32:01] Found vt - /usr/local/bin/vt
[00:32:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:32:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:32:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:32:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:32:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:32:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:32:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:32:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:42:13] This is snippy 4.6.0Show full stderr[00:42:13] This is snippy 4.6.0
[00:42:13] Written by Torsten Seemann
[00:42:13] Obtained from https://github.com/tseemann/snippy
[00:42:13] Detected operating system: linux
[00:42:13] Enabling bundled linux tools.
[00:42:13] Found bwa - /usr/local/bin/bwa
[00:42:13] Found bcftools - /usr/local/bin/bcftools
[00:42:13] Found samtools - /usr/local/bin/samtools
[00:42:13] Found java - /usr/local/bin/java
[00:42:13] Found snpEff - /usr/local/bin/snpEff
[00:42:13] Found samclip - /usr/local/bin/samclip
[00:42:13] Found seqtk - /usr/local/bin/seqtk
[00:42:13] Found parallel - /usr/local/bin/parallel
[00:42:13] Found freebayes - /usr/local/bin/freebayes
[00:42:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:42:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:42:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:42:13] Found vcfuniq - /usr/local/bin/vcfuniq
[00:42:13] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:42:13] Found gzip - /bin/gzip
[00:42:13] Found vt - /usr/local/bin/vt
[00:42:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:42:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:42:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:42:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:42:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:42:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:42:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:42:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:32:19] This is snippy 4.6.0Show full stderr[00:32:19] This is snippy 4.6.0
[00:32:19] Written by Torsten Seemann
[00:32:19] Obtained from https://github.com/tseemann/snippy
[00:32:19] Detected operating system: linux
[00:32:19] Enabling bundled linux tools.
[00:32:19] Found bwa - /usr/local/bin/bwa
[00:32:19] Found bcftools - /usr/local/bin/bcftools
[00:32:19] Found samtools - /usr/local/bin/samtools
[00:32:19] Found java - /usr/local/bin/java
[00:32:19] Found snpEff - /usr/local/bin/snpEff
[00:32:19] Found samclip - /usr/local/bin/samclip
[00:32:19] Found seqtk - /usr/local/bin/seqtk
[00:32:19] Found parallel - /usr/local/bin/parallel
[00:32:19] Found freebayes - /usr/local/bin/freebayes
[00:32:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:32:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:32:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:32:19] Found vcfuniq - /usr/local/bin/vcfuniq
[00:32:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:32:19] Found gzip - /bin/gzip
[00:32:19] Found vt - /usr/local/bin/vt
[00:32:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:32:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:32:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:32:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:32:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:32:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:32:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:32:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:32:34] This is snippy 4.6.0Show full stderr[00:32:34] This is snippy 4.6.0
[00:32:34] Written by Torsten Seemann
[00:32:34] Obtained from https://github.com/tseemann/snippy
[00:32:34] Detected operating system: linux
[00:32:34] Enabling bundled linux tools.
[00:32:34] Found bwa - /usr/local/bin/bwa
[00:32:34] Found bcftools - /usr/local/bin/bcftools
[00:32:34] Found samtools - /usr/local/bin/samtools
[00:32:34] Found java - /usr/local/bin/java
[00:32:34] Found snpEff - /usr/local/bin/snpEff
[00:32:34] Found samclip - /usr/local/bin/samclip
[00:32:34] Found seqtk - /usr/local/bin/seqtk
[00:32:34] Found parallel - /usr/local/bin/parallel
[00:32:34] Found freebayes - /usr/local/bin/freebayes
[00:32:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:32:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:32:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:32:34] Found vcfuniq - /usr/local/bin/vcfuniq
[00:32:34] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:32:34] Found gzip - /bin/gzip
[00:32:34] Found vt - /usr/local/bin/vt
[00:32:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:32:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:32:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:32:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:32:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:32:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:32:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:32:35] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:59:36] This is snippy 4.6.0Show full stderr[00:59:36] This is snippy 4.6.0
[00:59:36] Written by Torsten Seemann
[00:59:36] Obtained from https://github.com/tseemann/snippy
[00:59:36] Detected operating system: linux
[00:59:36] Enabling bundled linux tools.
[00:59:36] Found bwa - /usr/local/bin/bwa
[00:59:36] Found bcftools - /usr/local/bin/bcftools
[00:59:36] Found samtools - /usr/local/bin/samtools
[00:59:36] Found java - /usr/local/bin/java
[00:59:36] Found snpEff - /usr/local/bin/snpEff
[00:59:36] Found samclip - /usr/local/bin/samclip
[00:59:36] Found seqtk - /usr/local/bin/seqtk
[00:59:36] Found parallel - /usr/local/bin/parallel
[00:59:36] Found freebayes - /usr/local/bin/freebayes
[00:59:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:59:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:59:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:59:36] Found vcfuniq - /usr/local/bin/vcfuniq
[00:59:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:59:36] Found gzip - /bin/gzip
[00:59:36] Found vt - /usr/local/bin/vt
[00:59:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:59:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:59:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:59:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:59:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:59:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:59:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:59:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:00:38] This is snippy 4.6.0Show full stderr[01:00:38] This is snippy 4.6.0
[01:00:38] Written by Torsten Seemann
[01:00:38] Obtained from https://github.com/tseemann/snippy
[01:00:38] Detected operating system: linux
[01:00:38] Enabling bundled linux tools.
[01:00:38] Found bwa - /usr/local/bin/bwa
[01:00:38] Found bcftools - /usr/local/bin/bcftools
[01:00:38] Found samtools - /usr/local/bin/samtools
[01:00:38] Found java - /usr/local/bin/java
[01:00:38] Found snpEff - /usr/local/bin/snpEff
[01:00:38] Found samclip - /usr/local/bin/samclip
[01:00:38] Found seqtk - /usr/local/bin/seqtk
[01:00:38] Found parallel - /usr/local/bin/parallel
[01:00:38] Found freebayes - /usr/local/bin/freebayes
[01:00:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:00:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:00:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:00:38] Found vcfuniq - /usr/local/bin/vcfuniq
[01:00:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:00:38] Found gzip - /bin/gzip
[01:00:38] Found vt - /usr/local/bin/vt
[01:00:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:00:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:00:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:00:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:00:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:00:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:00:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:00:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:05:35] This is snippy 4.6.0Show full stderr[01:05:35] This is snippy 4.6.0
[01:05:35] Written by Torsten Seemann
[01:05:35] Obtained from https://github.com/tseemann/snippy
[01:05:35] Detected operating system: linux
[01:05:35] Enabling bundled linux tools.
[01:05:35] Found bwa - /usr/local/bin/bwa
[01:05:35] Found bcftools - /usr/local/bin/bcftools
[01:05:35] Found samtools - /usr/local/bin/samtools
[01:05:35] Found java - /usr/local/bin/java
[01:05:35] Found snpEff - /usr/local/bin/snpEff
[01:05:35] Found samclip - /usr/local/bin/samclip
[01:05:35] Found seqtk - /usr/local/bin/seqtk
[01:05:35] Found parallel - /usr/local/bin/parallel
[01:05:35] Found freebayes - /usr/local/bin/freebayes
[01:05:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:05:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:05:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:05:35] Found vcfuniq - /usr/local/bin/vcfuniq
[01:05:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:05:35] Found gzip - /bin/gzip
[01:05:36] Found vt - /usr/local/bin/vt
[01:05:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:05:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:05:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:05:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:05:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:05:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:05:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:05:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:07:03] This is snippy 4.6.0Show full stderr[01:07:03] This is snippy 4.6.0
[01:07:03] Written by Torsten Seemann
[01:07:03] Obtained from https://github.com/tseemann/snippy
[01:07:03] Detected operating system: linux
[01:07:03] Enabling bundled linux tools.
[01:07:03] Found bwa - /usr/local/bin/bwa
[01:07:03] Found bcftools - /usr/local/bin/bcftools
[01:07:03] Found samtools - /usr/local/bin/samtools
[01:07:03] Found java - /usr/local/bin/java
[01:07:03] Found snpEff - /usr/local/bin/snpEff
[01:07:03] Found samclip - /usr/local/bin/samclip
[01:07:03] Found seqtk - /usr/local/bin/seqtk
[01:07:03] Found parallel - /usr/local/bin/parallel
[01:07:03] Found freebayes - /usr/local/bin/freebayes
[01:07:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:07:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:07:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:07:03] Found vcfuniq - /usr/local/bin/vcfuniq
[01:07:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:07:03] Found gzip - /bin/gzip
[01:07:03] Found vt - /usr/local/bin/vt
[01:07:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:07:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:07:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:07:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:07:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:07:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:07:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:07:04] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:12:27] This is snippy 4.6.0Show full stderr[01:12:27] This is snippy 4.6.0
[01:12:27] Written by Torsten Seemann
[01:12:27] Obtained from https://github.com/tseemann/snippy
[01:12:27] Detected operating system: linux
[01:12:27] Enabling bundled linux tools.
[01:12:27] Found bwa - /usr/local/bin/bwa
[01:12:27] Found bcftools - /usr/local/bin/bcftools
[01:12:27] Found samtools - /usr/local/bin/samtools
[01:12:27] Found java - /usr/local/bin/java
[01:12:27] Found snpEff - /usr/local/bin/snpEff
[01:12:27] Found samclip - /usr/local/bin/samclip
[01:12:27] Found seqtk - /usr/local/bin/seqtk
[01:12:27] Found parallel - /usr/local/bin/parallel
[01:12:27] Found freebayes - /usr/local/bin/freebayes
[01:12:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:12:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:12:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:12:27] Found vcfuniq - /usr/local/bin/vcfuniq
[01:12:27] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:12:27] Found gzip - /bin/gzip
[01:12:27] Found vt - /usr/local/bin/vt
[01:12:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:12:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:12:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:12:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:12:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:12:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:12:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:12:27] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:47:57] This is snippy 4.6.0Show full stderr[01:47:57] This is snippy 4.6.0
[01:47:57] Written by Torsten Seemann
[01:47:57] Obtained from https://github.com/tseemann/snippy
[01:47:57] Detected operating system: linux
[01:47:57] Enabling bundled linux tools.
[01:47:57] Found bwa - /usr/local/bin/bwa
[01:47:57] Found bcftools - /usr/local/bin/bcftools
[01:47:57] Found samtools - /usr/local/bin/samtools
[01:47:57] Found java - /usr/local/bin/java
[01:47:57] Found snpEff - /usr/local/bin/snpEff
[01:47:57] Found samclip - /usr/local/bin/samclip
[01:47:57] Found seqtk - /usr/local/bin/seqtk
[01:47:57] Found parallel - /usr/local/bin/parallel
[01:47:57] Found freebayes - /usr/local/bin/freebayes
[01:47:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:47:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:47:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:47:57] Found vcfuniq - /usr/local/bin/vcfuniq
[01:47:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:47:57] Found gzip - /bin/gzip
[01:47:57] Found vt - /usr/local/bin/vt
[01:47:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:47:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:47:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:47:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:47:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:47:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:47:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:47:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:06:28] This is snippy 4.6.0Show full stderr[02:06:28] This is snippy 4.6.0
[02:06:28] Written by Torsten Seemann
[02:06:28] Obtained from https://github.com/tseemann/snippy
[02:06:28] Detected operating system: linux
[02:06:28] Enabling bundled linux tools.
[02:06:28] Found bwa - /usr/local/bin/bwa
[02:06:28] Found bcftools - /usr/local/bin/bcftools
[02:06:28] Found samtools - /usr/local/bin/samtools
[02:06:28] Found java - /usr/local/bin/java
[02:06:28] Found snpEff - /usr/local/bin/snpEff
[02:06:28] Found samclip - /usr/local/bin/samclip
[02:06:28] Found seqtk - /usr/local/bin/seqtk
[02:06:28] Found parallel - /usr/local/bin/parallel
[02:06:28] Found freebayes - /usr/local/bin/freebayes
[02:06:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:06:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:06:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:06:28] Found vcfuniq - /usr/local/bin/vcfuniq
[02:06:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:06:28] Found gzip - /bin/gzip
[02:06:28] Found vt - /usr/local/bin/vt
[02:06:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:06:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:06:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:06:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:06:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:06:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:06:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:06:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:48:12] This is snippy 4.6.0Show full stderr[01:48:12] This is snippy 4.6.0
[01:48:12] Written by Torsten Seemann
[01:48:12] Obtained from https://github.com/tseemann/snippy
[01:48:12] Detected operating system: linux
[01:48:12] Enabling bundled linux tools.
[01:48:12] Found bwa - /usr/local/bin/bwa
[01:48:12] Found bcftools - /usr/local/bin/bcftools
[01:48:12] Found samtools - /usr/local/bin/samtools
[01:48:12] Found java - /usr/local/bin/java
[01:48:12] Found snpEff - /usr/local/bin/snpEff
[01:48:12] Found samclip - /usr/local/bin/samclip
[01:48:12] Found seqtk - /usr/local/bin/seqtk
[01:48:12] Found parallel - /usr/local/bin/parallel
[01:48:12] Found freebayes - /usr/local/bin/freebayes
[01:48:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:48:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:48:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:48:12] Found vcfuniq - /usr/local/bin/vcfuniq
[01:48:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:48:12] Found gzip - /bin/gzip
[01:48:12] Found vt - /usr/local/bin/vt
[01:48:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:48:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:48:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:48:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:48:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:48:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:48:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:48:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:48:31] This is snippy 4.6.0Show full stderr[01:48:31] This is snippy 4.6.0
[01:48:31] Written by Torsten Seemann
[01:48:31] Obtained from https://github.com/tseemann/snippy
[01:48:31] Detected operating system: linux
[01:48:31] Enabling bundled linux tools.
[01:48:31] Found bwa - /usr/local/bin/bwa
[01:48:31] Found bcftools - /usr/local/bin/bcftools
[01:48:31] Found samtools - /usr/local/bin/samtools
[01:48:31] Found java - /usr/local/bin/java
[01:48:31] Found snpEff - /usr/local/bin/snpEff
[01:48:31] Found samclip - /usr/local/bin/samclip
[01:48:31] Found seqtk - /usr/local/bin/seqtk
[01:48:31] Found parallel - /usr/local/bin/parallel
[01:48:31] Found freebayes - /usr/local/bin/freebayes
[01:48:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:48:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:48:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:48:31] Found vcfuniq - /usr/local/bin/vcfuniq
[01:48:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:48:31] Found gzip - /bin/gzip
[01:48:31] Found vt - /usr/local/bin/vt
[01:48:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:48:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:48:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:48:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:48:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:48:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:48:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:48:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:50:49] This is snippy 4.6.0Show full stderr[01:50:49] This is snippy 4.6.0
[01:50:49] Written by Torsten Seemann
[01:50:49] Obtained from https://github.com/tseemann/snippy
[01:50:49] Detected operating system: linux
[01:50:49] Enabling bundled linux tools.
[01:50:49] Found bwa - /usr/local/bin/bwa
[01:50:49] Found bcftools - /usr/local/bin/bcftools
[01:50:49] Found samtools - /usr/local/bin/samtools
[01:50:49] Found java - /usr/local/bin/java
[01:50:49] Found snpEff - /usr/local/bin/snpEff
[01:50:49] Found samclip - /usr/local/bin/samclip
[01:50:49] Found seqtk - /usr/local/bin/seqtk
[01:50:49] Found parallel - /usr/local/bin/parallel
[01:50:49] Found freebayes - /usr/local/bin/freebayes
[01:50:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:50:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:50:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:50:49] Found vcfuniq - /usr/local/bin/vcfuniq
[01:50:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:50:49] Found gzip - /bin/gzip
[01:50:49] Found vt - /usr/local/bin/vt
[01:50:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:50:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:50:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:50:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:50:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:50:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:50:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:50:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:56:27] This is snippy 4.6.0Show full stderr[01:56:27] This is snippy 4.6.0
[01:56:27] Written by Torsten Seemann
[01:56:27] Obtained from https://github.com/tseemann/snippy
[01:56:27] Detected operating system: linux
[01:56:27] Enabling bundled linux tools.
[01:56:27] Found bwa - /usr/local/bin/bwa
[01:56:27] Found bcftools - /usr/local/bin/bcftools
[01:56:27] Found samtools - /usr/local/bin/samtools
[01:56:27] Found java - /usr/local/bin/java
[01:56:27] Found snpEff - /usr/local/bin/snpEff
[01:56:28] Found samclip - /usr/local/bin/samclip
[01:56:28] Found seqtk - /usr/local/bin/seqtk
[01:56:28] Found parallel - /usr/local/bin/parallel
[01:56:28] Found freebayes - /usr/local/bin/freebayes
[01:56:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:56:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:56:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:56:28] Found vcfuniq - /usr/local/bin/vcfuniq
[01:56:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:56:28] Found gzip - /bin/gzip
[01:56:28] Found vt - /usr/local/bin/vt
[01:56:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:56:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:56:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:56:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:56:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:56:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:56:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:56:28] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:58:23] This is snippy 4.6.0Show full stderr[01:58:23] This is snippy 4.6.0
[01:58:23] Written by Torsten Seemann
[01:58:23] Obtained from https://github.com/tseemann/snippy
[01:58:23] Detected operating system: linux
[01:58:23] Enabling bundled linux tools.
[01:58:23] Found bwa - /usr/local/bin/bwa
[01:58:23] Found bcftools - /usr/local/bin/bcftools
[01:58:23] Found samtools - /usr/local/bin/samtools
[01:58:23] Found java - /usr/local/bin/java
[01:58:23] Found snpEff - /usr/local/bin/snpEff
[01:58:23] Found samclip - /usr/local/bin/samclip
[01:58:23] Found seqtk - /usr/local/bin/seqtk
[01:58:23] Found parallel - /usr/local/bin/parallel
[01:58:23] Found freebayes - /usr/local/bin/freebayes
[01:58:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:58:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:58:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:58:23] Found vcfuniq - /usr/local/bin/vcfuniq
[01:58:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:58:23] Found gzip - /bin/gzip
[01:58:23] Found vt - /usr/local/bin/vt
[01:58:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:58:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:58:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:58:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:58:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:58:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:58:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:58:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:58:52] This is snippy 4.6.0Show full stderr[01:58:52] This is snippy 4.6.0
[01:58:52] Written by Torsten Seemann
[01:58:52] Obtained from https://github.com/tseemann/snippy
[01:58:52] Detected operating system: linux
[01:58:52] Enabling bundled linux tools.
[01:58:52] Found bwa - /usr/local/bin/bwa
[01:58:52] Found bcftools - /usr/local/bin/bcftools
[01:58:52] Found samtools - /usr/local/bin/samtools
[01:58:52] Found java - /usr/local/bin/java
[01:58:52] Found snpEff - /usr/local/bin/snpEff
[01:58:52] Found samclip - /usr/local/bin/samclip
[01:58:52] Found seqtk - /usr/local/bin/seqtk
[01:58:52] Found parallel - /usr/local/bin/parallel
[01:58:52] Found freebayes - /usr/local/bin/freebayes
[01:58:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:58:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:58:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:58:52] Found vcfuniq - /usr/local/bin/vcfuniq
[01:58:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:58:52] Found gzip - /bin/gzip
[01:58:52] Found vt - /usr/local/bin/vt
[01:58:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:58:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:58:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:58:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:58:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:58:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:58:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:58:53] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:59:00] This is snippy 4.6.0Show full stderr[01:59:00] This is snippy 4.6.0
[01:59:00] Written by Torsten Seemann
[01:59:00] Obtained from https://github.com/tseemann/snippy
[01:59:00] Detected operating system: linux
[01:59:00] Enabling bundled linux tools.
[01:59:00] Found bwa - /usr/local/bin/bwa
[01:59:00] Found bcftools - /usr/local/bin/bcftools
[01:59:00] Found samtools - /usr/local/bin/samtools
[01:59:00] Found java - /usr/local/bin/java
[01:59:00] Found snpEff - /usr/local/bin/snpEff
[01:59:00] Found samclip - /usr/local/bin/samclip
[01:59:00] Found seqtk - /usr/local/bin/seqtk
[01:59:00] Found parallel - /usr/local/bin/parallel
[01:59:00] Found freebayes - /usr/local/bin/freebayes
[01:59:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:59:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:59:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:59:00] Found vcfuniq - /usr/local/bin/vcfuniq
[01:59:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:59:00] Found gzip - /bin/gzip
[01:59:00] Found vt - /usr/local/bin/vt
[01:59:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:59:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:59:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:59:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:59:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:59:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:59:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:59:01] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:59:09] This is snippy 4.6.0Show full stderr[01:59:09] This is snippy 4.6.0
[01:59:09] Written by Torsten Seemann
[01:59:09] Obtained from https://github.com/tseemann/snippy
[01:59:09] Detected operating system: linux
[01:59:09] Enabling bundled linux tools.
[01:59:09] Found bwa - /usr/local/bin/bwa
[01:59:09] Found bcftools - /usr/local/bin/bcftools
[01:59:09] Found samtools - /usr/local/bin/samtools
[01:59:09] Found java - /usr/local/bin/java
[01:59:09] Found snpEff - /usr/local/bin/snpEff
[01:59:09] Found samclip - /usr/local/bin/samclip
[01:59:09] Found seqtk - /usr/local/bin/seqtk
[01:59:09] Found parallel - /usr/local/bin/parallel
[01:59:09] Found freebayes - /usr/local/bin/freebayes
[01:59:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:59:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:59:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:59:09] Found vcfuniq - /usr/local/bin/vcfuniq
[01:59:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:59:09] Found gzip - /bin/gzip
[01:59:09] Found vt - /usr/local/bin/vt
[01:59:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:59:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:59:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:59:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:59:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:59:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:59:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:59:10] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:59:16] This is snippy 4.6.0Show full stderr[01:59:16] This is snippy 4.6.0
[01:59:16] Written by Torsten Seemann
[01:59:16] Obtained from https://github.com/tseemann/snippy
[01:59:16] Detected operating system: linux
[01:59:16] Enabling bundled linux tools.
[01:59:16] Found bwa - /usr/local/bin/bwa
[01:59:16] Found bcftools - /usr/local/bin/bcftools
[01:59:16] Found samtools - /usr/local/bin/samtools
[01:59:16] Found java - /usr/local/bin/java
[01:59:16] Found snpEff - /usr/local/bin/snpEff
[01:59:16] Found samclip - /usr/local/bin/samclip
[01:59:16] Found seqtk - /usr/local/bin/seqtk
[01:59:16] Found parallel - /usr/local/bin/parallel
[01:59:16] Found freebayes - /usr/local/bin/freebayes
[01:59:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:59:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:59:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:59:16] Found vcfuniq - /usr/local/bin/vcfuniq
[01:59:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:59:16] Found gzip - /bin/gzip
[01:59:16] Found vt - /usr/local/bin/vt
[01:59:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:59:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:59:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:59:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:59:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:59:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:59:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:59:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:59:31] This is snippy 4.6.0Show full stderr[01:59:31] This is snippy 4.6.0
[01:59:31] Written by Torsten Seemann
[01:59:31] Obtained from https://github.com/tseemann/snippy
[01:59:31] Detected operating system: linux
[01:59:31] Enabling bundled linux tools.
[01:59:31] Found bwa - /usr/local/bin/bwa
[01:59:31] Found bcftools - /usr/local/bin/bcftools
[01:59:31] Found samtools - /usr/local/bin/samtools
[01:59:31] Found java - /usr/local/bin/java
[01:59:31] Found snpEff - /usr/local/bin/snpEff
[01:59:31] Found samclip - /usr/local/bin/samclip
[01:59:31] Found seqtk - /usr/local/bin/seqtk
[01:59:31] Found parallel - /usr/local/bin/parallel
[01:59:31] Found freebayes - /usr/local/bin/freebayes
[01:59:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:59:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:59:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:59:31] Found vcfuniq - /usr/local/bin/vcfuniq
[01:59:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:59:31] Found gzip - /bin/gzip
[01:59:31] Found vt - /usr/local/bin/vt
[01:59:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:59:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:59:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:59:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:59:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:59:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:59:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:59:32] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:59:54] This is snippy 4.6.0Show full stderr[01:59:54] This is snippy 4.6.0
[01:59:54] Written by Torsten Seemann
[01:59:54] Obtained from https://github.com/tseemann/snippy
[01:59:54] Detected operating system: linux
[01:59:54] Enabling bundled linux tools.
[01:59:54] Found bwa - /usr/local/bin/bwa
[01:59:54] Found bcftools - /usr/local/bin/bcftools
[01:59:54] Found samtools - /usr/local/bin/samtools
[01:59:54] Found java - /usr/local/bin/java
[01:59:54] Found snpEff - /usr/local/bin/snpEff
[01:59:54] Found samclip - /usr/local/bin/samclip
[01:59:54] Found seqtk - /usr/local/bin/seqtk
[01:59:54] Found parallel - /usr/local/bin/parallel
[01:59:54] Found freebayes - /usr/local/bin/freebayes
[01:59:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:59:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:59:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:59:54] Found vcfuniq - /usr/local/bin/vcfuniq
[01:59:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:59:54] Found gzip - /bin/gzip
[01:59:54] Found vt - /usr/local/bin/vt
[01:59:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:59:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:59:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:59:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:59:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:59:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:59:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:59:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:00:42] This is snippy 4.6.0Show full stderr[02:00:42] This is snippy 4.6.0
[02:00:42] Written by Torsten Seemann
[02:00:42] Obtained from https://github.com/tseemann/snippy
[02:00:42] Detected operating system: linux
[02:00:42] Enabling bundled linux tools.
[02:00:42] Found bwa - /usr/local/bin/bwa
[02:00:42] Found bcftools - /usr/local/bin/bcftools
[02:00:42] Found samtools - /usr/local/bin/samtools
[02:00:42] Found java - /usr/local/bin/java
[02:00:42] Found snpEff - /usr/local/bin/snpEff
[02:00:42] Found samclip - /usr/local/bin/samclip
[02:00:42] Found seqtk - /usr/local/bin/seqtk
[02:00:42] Found parallel - /usr/local/bin/parallel
[02:00:42] Found freebayes - /usr/local/bin/freebayes
[02:00:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:00:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:00:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:00:42] Found vcfuniq - /usr/local/bin/vcfuniq
[02:00:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:00:42] Found gzip - /bin/gzip
[02:00:42] Found vt - /usr/local/bin/vt
[02:00:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:00:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:00:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:00:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:00:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:00:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:00:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:00:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:02:42] This is snippy 4.6.0Show full stderr[02:02:42] This is snippy 4.6.0
[02:02:42] Written by Torsten Seemann
[02:02:42] Obtained from https://github.com/tseemann/snippy
[02:02:42] Detected operating system: linux
[02:02:42] Enabling bundled linux tools.
[02:02:42] Found bwa - /usr/local/bin/bwa
[02:02:42] Found bcftools - /usr/local/bin/bcftools
[02:02:42] Found samtools - /usr/local/bin/samtools
[02:02:42] Found java - /usr/local/bin/java
[02:02:42] Found snpEff - /usr/local/bin/snpEff
[02:02:42] Found samclip - /usr/local/bin/samclip
[02:02:42] Found seqtk - /usr/local/bin/seqtk
[02:02:42] Found parallel - /usr/local/bin/parallel
[02:02:42] Found freebayes - /usr/local/bin/freebayes
[02:02:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:02:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:02:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:02:42] Found vcfuniq - /usr/local/bin/vcfuniq
[02:02:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:02:42] Found gzip - /bin/gzip
[02:02:42] Found vt - /usr/local/bin/vt
[02:02:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:02:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:02:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:02:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:02:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:02:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:02:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:02:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:03:57] This is snippy 4.6.0Show full stderr[02:03:57] This is snippy 4.6.0
[02:03:57] Written by Torsten Seemann
[02:03:57] Obtained from https://github.com/tseemann/snippy
[02:03:57] Detected operating system: linux
[02:03:57] Enabling bundled linux tools.
[02:03:58] Found bwa - /usr/local/bin/bwa
[02:03:58] Found bcftools - /usr/local/bin/bcftools
[02:03:58] Found samtools - /usr/local/bin/samtools
[02:03:58] Found java - /usr/local/bin/java
[02:03:58] Found snpEff - /usr/local/bin/snpEff
[02:03:58] Found samclip - /usr/local/bin/samclip
[02:03:58] Found seqtk - /usr/local/bin/seqtk
[02:03:58] Found parallel - /usr/local/bin/parallel
[02:03:58] Found freebayes - /usr/local/bin/freebayes
[02:03:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:03:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:03:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:03:58] Found vcfuniq - /usr/local/bin/vcfuniq
[02:03:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:03:58] Found gzip - /bin/gzip
[02:03:58] Found vt - /usr/local/bin/vt
[02:03:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:03:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:03:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:03:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:03:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:04:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:04:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:04:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:49:02] This is snippy 4.6.0Show full stderr[00:49:02] This is snippy 4.6.0
[00:49:02] Written by Torsten Seemann
[00:49:02] Obtained from https://github.com/tseemann/snippy
[00:49:02] Detected operating system: linux
[00:49:02] Enabling bundled linux tools.
[00:49:02] Found bwa - /usr/local/bin/bwa
[00:49:02] Found bcftools - /usr/local/bin/bcftools
[00:49:02] Found samtools - /usr/local/bin/samtools
[00:49:02] Found java - /usr/local/bin/java
[00:49:02] Found snpEff - /usr/local/bin/snpEff
[00:49:02] Found samclip - /usr/local/bin/samclip
[00:49:02] Found seqtk - /usr/local/bin/seqtk
[00:49:02] Found parallel - /usr/local/bin/parallel
[00:49:02] Found freebayes - /usr/local/bin/freebayes
[00:49:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:49:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:49:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:49:02] Found vcfuniq - /usr/local/bin/vcfuniq
[00:49:02] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:49:02] Found gzip - /bin/gzip
[00:49:02] Found vt - /usr/local/bin/vt
[00:49:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:49:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:49:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:49:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:49:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:49:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:49:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:49:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:53:22] This is snippy 4.6.0Show full stderr[00:53:22] This is snippy 4.6.0
[00:53:22] Written by Torsten Seemann
[00:53:22] Obtained from https://github.com/tseemann/snippy
[00:53:22] Detected operating system: linux
[00:53:22] Enabling bundled linux tools.
[00:53:22] Found bwa - /usr/local/bin/bwa
[00:53:22] Found bcftools - /usr/local/bin/bcftools
[00:53:22] Found samtools - /usr/local/bin/samtools
[00:53:22] Found java - /usr/local/bin/java
[00:53:22] Found snpEff - /usr/local/bin/snpEff
[00:53:22] Found samclip - /usr/local/bin/samclip
[00:53:22] Found seqtk - /usr/local/bin/seqtk
[00:53:22] Found parallel - /usr/local/bin/parallel
[00:53:22] Found freebayes - /usr/local/bin/freebayes
[00:53:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:53:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:53:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:53:22] Found vcfuniq - /usr/local/bin/vcfuniq
[00:53:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:53:22] Found gzip - /bin/gzip
[00:53:22] Found vt - /usr/local/bin/vt
[00:53:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:53:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:53:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:53:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:53:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:53:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:53:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:53:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:07:35] This is snippy 4.6.0Show full stderr[01:07:35] This is snippy 4.6.0
[01:07:35] Written by Torsten Seemann
[01:07:35] Obtained from https://github.com/tseemann/snippy
[01:07:35] Detected operating system: linux
[01:07:35] Enabling bundled linux tools.
[01:07:36] Found bwa - /usr/local/bin/bwa
[01:07:36] Found bcftools - /usr/local/bin/bcftools
[01:07:36] Found samtools - /usr/local/bin/samtools
[01:07:36] Found java - /usr/local/bin/java
[01:07:36] Found snpEff - /usr/local/bin/snpEff
[01:07:36] Found samclip - /usr/local/bin/samclip
[01:07:36] Found seqtk - /usr/local/bin/seqtk
[01:07:36] Found parallel - /usr/local/bin/parallel
[01:07:36] Found freebayes - /usr/local/bin/freebayes
[01:07:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:07:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:07:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:07:36] Found vcfuniq - /usr/local/bin/vcfuniq
[01:07:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:07:36] Found gzip - /bin/gzip
[01:07:36] Found vt - /usr/local/bin/vt
[01:07:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:07:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:07:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:07:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:07:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:07:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:07:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:07:37] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:56:40] This is snippy 4.6.0Show full stderr[00:56:40] This is snippy 4.6.0
[00:56:40] Written by Torsten Seemann
[00:56:40] Obtained from https://github.com/tseemann/snippy
[00:56:40] Detected operating system: linux
[00:56:40] Enabling bundled linux tools.
[00:56:40] Found bwa - /usr/local/bin/bwa
[00:56:40] Found bcftools - /usr/local/bin/bcftools
[00:56:40] Found samtools - /usr/local/bin/samtools
[00:56:40] Found java - /usr/local/bin/java
[00:56:40] Found snpEff - /usr/local/bin/snpEff
[00:56:40] Found samclip - /usr/local/bin/samclip
[00:56:40] Found seqtk - /usr/local/bin/seqtk
[00:56:40] Found parallel - /usr/local/bin/parallel
[00:56:40] Found freebayes - /usr/local/bin/freebayes
[00:56:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:56:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:56:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:56:40] Found vcfuniq - /usr/local/bin/vcfuniq
[00:56:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:56:41] Found gzip - /bin/gzip
[00:56:41] Found vt - /usr/local/bin/vt
[00:56:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:56:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:56:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:56:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:56:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:56:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:56:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:56:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:34:42] This is snippy 4.6.0Show full stderr[00:34:42] This is snippy 4.6.0
[00:34:42] Written by Torsten Seemann
[00:34:42] Obtained from https://github.com/tseemann/snippy
[00:34:42] Detected operating system: linux
[00:34:42] Enabling bundled linux tools.
[00:34:42] Found bwa - /usr/local/bin/bwa
[00:34:42] Found bcftools - /usr/local/bin/bcftools
[00:34:42] Found samtools - /usr/local/bin/samtools
[00:34:42] Found java - /usr/local/bin/java
[00:34:42] Found snpEff - /usr/local/bin/snpEff
[00:34:42] Found samclip - /usr/local/bin/samclip
[00:34:42] Found seqtk - /usr/local/bin/seqtk
[00:34:42] Found parallel - /usr/local/bin/parallel
[00:34:42] Found freebayes - /usr/local/bin/freebayes
[00:34:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:34:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:34:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:34:42] Found vcfuniq - /usr/local/bin/vcfuniq
[00:34:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:34:42] Found gzip - /bin/gzip
[00:34:42] Found vt - /usr/local/bin/vt
[00:34:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:34:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:34:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:34:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:34:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:34:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:34:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:34:43] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:34:54] This is snippy 4.6.0Show full stderr[00:34:54] This is snippy 4.6.0
[00:34:54] Written by Torsten Seemann
[00:34:54] Obtained from https://github.com/tseemann/snippy
[00:34:54] Detected operating system: linux
[00:34:54] Enabling bundled linux tools.
[00:34:54] Found bwa - /usr/local/bin/bwa
[00:34:54] Found bcftools - /usr/local/bin/bcftools
[00:34:54] Found samtools - /usr/local/bin/samtools
[00:34:54] Found java - /usr/local/bin/java
[00:34:54] Found snpEff - /usr/local/bin/snpEff
[00:34:54] Found samclip - /usr/local/bin/samclip
[00:34:54] Found seqtk - /usr/local/bin/seqtk
[00:34:54] Found parallel - /usr/local/bin/parallel
[00:34:54] Found freebayes - /usr/local/bin/freebayes
[00:34:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:34:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:34:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:34:54] Found vcfuniq - /usr/local/bin/vcfuniq
[00:34:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:34:54] Found gzip - /bin/gzip
[00:34:54] Found vt - /usr/local/bin/vt
[00:34:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:34:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:34:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:34:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:34:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:34:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:34:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:34:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:38:35] This is snippy 4.6.0Show full stderr[00:38:35] This is snippy 4.6.0
[00:38:35] Written by Torsten Seemann
[00:38:35] Obtained from https://github.com/tseemann/snippy
[00:38:35] Detected operating system: linux
[00:38:35] Enabling bundled linux tools.
[00:38:35] Found bwa - /usr/local/bin/bwa
[00:38:35] Found bcftools - /usr/local/bin/bcftools
[00:38:35] Found samtools - /usr/local/bin/samtools
[00:38:35] Found java - /usr/local/bin/java
[00:38:35] Found snpEff - /usr/local/bin/snpEff
[00:38:35] Found samclip - /usr/local/bin/samclip
[00:38:35] Found seqtk - /usr/local/bin/seqtk
[00:38:35] Found parallel - /usr/local/bin/parallel
[00:38:35] Found freebayes - /usr/local/bin/freebayes
[00:38:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:38:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:38:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:38:35] Found vcfuniq - /usr/local/bin/vcfuniq
[00:38:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:38:35] Found gzip - /bin/gzip
[00:38:35] Found vt - /usr/local/bin/vt
[00:38:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:38:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:38:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:38:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:38:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:38:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:38:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:38:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:43:20] This is snippy 4.6.0Show full stderr[00:43:20] This is snippy 4.6.0
[00:43:20] Written by Torsten Seemann
[00:43:20] Obtained from https://github.com/tseemann/snippy
[00:43:20] Detected operating system: linux
[00:43:20] Enabling bundled linux tools.
[00:43:20] Found bwa - /usr/local/bin/bwa
[00:43:20] Found bcftools - /usr/local/bin/bcftools
[00:43:20] Found samtools - /usr/local/bin/samtools
[00:43:20] Found java - /usr/local/bin/java
[00:43:20] Found snpEff - /usr/local/bin/snpEff
[00:43:20] Found samclip - /usr/local/bin/samclip
[00:43:20] Found seqtk - /usr/local/bin/seqtk
[00:43:20] Found parallel - /usr/local/bin/parallel
[00:43:20] Found freebayes - /usr/local/bin/freebayes
[00:43:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:43:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:43:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:43:20] Found vcfuniq - /usr/local/bin/vcfuniq
[00:43:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:43:20] Found gzip - /bin/gzip
[00:43:20] Found vt - /usr/local/bin/vt
[00:43:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:43:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:43:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:43:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:43:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:43:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:43:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:43:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:43:17] This is snippy 4.6.0Show full stderr[00:43:17] This is snippy 4.6.0
[00:43:17] Written by Torsten Seemann
[00:43:17] Obtained from https://github.com/tseemann/snippy
[00:43:17] Detected operating system: linux
[00:43:17] Enabling bundled linux tools.
[00:43:17] Found bwa - /usr/local/bin/bwa
[00:43:17] Found bcftools - /usr/local/bin/bcftools
[00:43:17] Found samtools - /usr/local/bin/samtools
[00:43:17] Found java - /usr/local/bin/java
[00:43:18] Found snpEff - /usr/local/bin/snpEff
[00:43:18] Found samclip - /usr/local/bin/samclip
[00:43:18] Found seqtk - /usr/local/bin/seqtk
[00:43:18] Found parallel - /usr/local/bin/parallel
[00:43:18] Found freebayes - /usr/local/bin/freebayes
[00:43:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:43:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:43:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:43:18] Found vcfuniq - /usr/local/bin/vcfuniq
[00:43:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:43:18] Found gzip - /bin/gzip
[00:43:18] Found vt - /usr/local/bin/vt
[00:43:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:43:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:43:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:43:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:43:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:43:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:43:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:43:19] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:06:40] This is snippy 4.6.0Show full stderr[01:06:40] This is snippy 4.6.0
[01:06:40] Written by Torsten Seemann
[01:06:40] Obtained from https://github.com/tseemann/snippy
[01:06:40] Detected operating system: linux
[01:06:40] Enabling bundled linux tools.
[01:06:40] Found bwa - /usr/local/bin/bwa
[01:06:40] Found bcftools - /usr/local/bin/bcftools
[01:06:40] Found samtools - /usr/local/bin/samtools
[01:06:40] Found java - /usr/local/bin/java
[01:06:40] Found snpEff - /usr/local/bin/snpEff
[01:06:40] Found samclip - /usr/local/bin/samclip
[01:06:40] Found seqtk - /usr/local/bin/seqtk
[01:06:40] Found parallel - /usr/local/bin/parallel
[01:06:40] Found freebayes - /usr/local/bin/freebayes
[01:06:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:06:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:06:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:06:40] Found vcfuniq - /usr/local/bin/vcfuniq
[01:06:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:06:40] Found gzip - /bin/gzip
[01:06:40] Found vt - /usr/local/bin/vt
[01:06:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:06:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:06:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:06:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:06:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:06:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:06:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:06:41] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:11:56] This is snippy 4.6.0Show full stderr[01:11:56] This is snippy 4.6.0
[01:11:56] Written by Torsten Seemann
[01:11:56] Obtained from https://github.com/tseemann/snippy
[01:11:56] Detected operating system: linux
[01:11:56] Enabling bundled linux tools.
[01:11:56] Found bwa - /usr/local/bin/bwa
[01:11:56] Found bcftools - /usr/local/bin/bcftools
[01:11:56] Found samtools - /usr/local/bin/samtools
[01:11:56] Found java - /usr/local/bin/java
[01:11:56] Found snpEff - /usr/local/bin/snpEff
[01:11:56] Found samclip - /usr/local/bin/samclip
[01:11:56] Found seqtk - /usr/local/bin/seqtk
[01:11:56] Found parallel - /usr/local/bin/parallel
[01:11:56] Found freebayes - /usr/local/bin/freebayes
[01:11:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:11:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:11:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:11:56] Found vcfuniq - /usr/local/bin/vcfuniq
[01:11:56] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:11:56] Found gzip - /bin/gzip
[01:11:56] Found vt - /usr/local/bin/vt
[01:11:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:11:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:11:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:11:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:11:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:11:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:11:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:11:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:53:38] This is snippy 4.6.0Show full stderr[01:53:38] This is snippy 4.6.0
[01:53:38] Written by Torsten Seemann
[01:53:38] Obtained from https://github.com/tseemann/snippy
[01:53:38] Detected operating system: linux
[01:53:38] Enabling bundled linux tools.
[01:53:38] Found bwa - /usr/local/bin/bwa
[01:53:38] Found bcftools - /usr/local/bin/bcftools
[01:53:38] Found samtools - /usr/local/bin/samtools
[01:53:38] Found java - /usr/local/bin/java
[01:53:38] Found snpEff - /usr/local/bin/snpEff
[01:53:38] Found samclip - /usr/local/bin/samclip
[01:53:38] Found seqtk - /usr/local/bin/seqtk
[01:53:38] Found parallel - /usr/local/bin/parallel
[01:53:38] Found freebayes - /usr/local/bin/freebayes
[01:53:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:53:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:53:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:53:38] Found vcfuniq - /usr/local/bin/vcfuniq
[01:53:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:53:38] Found gzip - /bin/gzip
[01:53:38] Found vt - /usr/local/bin/vt
[01:53:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:53:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:53:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:53:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:53:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:53:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:53:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:53:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:23:57] This is snippy 4.6.0Show full stderr[01:23:57] This is snippy 4.6.0
[01:23:57] Written by Torsten Seemann
[01:23:57] Obtained from https://github.com/tseemann/snippy
[01:23:57] Detected operating system: linux
[01:23:57] Enabling bundled linux tools.
[01:23:57] Found bwa - /usr/local/bin/bwa
[01:23:57] Found bcftools - /usr/local/bin/bcftools
[01:23:57] Found samtools - /usr/local/bin/samtools
[01:23:57] Found java - /usr/local/bin/java
[01:23:57] Found snpEff - /usr/local/bin/snpEff
[01:23:57] Found samclip - /usr/local/bin/samclip
[01:23:57] Found seqtk - /usr/local/bin/seqtk
[01:23:57] Found parallel - /usr/local/bin/parallel
[01:23:57] Found freebayes - /usr/local/bin/freebayes
[01:23:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:23:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:23:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:23:57] Found vcfuniq - /usr/local/bin/vcfuniq
[01:23:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:23:57] Found gzip - /bin/gzip
[01:23:57] Found vt - /usr/local/bin/vt
[01:23:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:23:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:23:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:23:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:23:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:23:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:23:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:23:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:24:01] This is snippy 4.6.0Show full stderr[01:24:01] This is snippy 4.6.0
[01:24:01] Written by Torsten Seemann
[01:24:01] Obtained from https://github.com/tseemann/snippy
[01:24:01] Detected operating system: linux
[01:24:01] Enabling bundled linux tools.
[01:24:01] Found bwa - /usr/local/bin/bwa
[01:24:01] Found bcftools - /usr/local/bin/bcftools
[01:24:01] Found samtools - /usr/local/bin/samtools
[01:24:01] Found java - /usr/local/bin/java
[01:24:01] Found snpEff - /usr/local/bin/snpEff
[01:24:01] Found samclip - /usr/local/bin/samclip
[01:24:01] Found seqtk - /usr/local/bin/seqtk
[01:24:01] Found parallel - /usr/local/bin/parallel
[01:24:01] Found freebayes - /usr/local/bin/freebayes
[01:24:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:24:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:24:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:24:01] Found vcfuniq - /usr/local/bin/vcfuniq
[01:24:01] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:24:01] Found gzip - /bin/gzip
[01:24:01] Found vt - /usr/local/bin/vt
[01:24:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:24:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:24:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:24:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:24:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:24:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:24:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:24:02] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:24:12] This is snippy 4.6.0Show full stderr[01:24:12] This is snippy 4.6.0
[01:24:12] Written by Torsten Seemann
[01:24:12] Obtained from https://github.com/tseemann/snippy
[01:24:12] Detected operating system: linux
[01:24:12] Enabling bundled linux tools.
[01:24:12] Found bwa - /usr/local/bin/bwa
[01:24:12] Found bcftools - /usr/local/bin/bcftools
[01:24:12] Found samtools - /usr/local/bin/samtools
[01:24:12] Found java - /usr/local/bin/java
[01:24:12] Found snpEff - /usr/local/bin/snpEff
[01:24:12] Found samclip - /usr/local/bin/samclip
[01:24:12] Found seqtk - /usr/local/bin/seqtk
[01:24:12] Found parallel - /usr/local/bin/parallel
[01:24:12] Found freebayes - /usr/local/bin/freebayes
[01:24:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:24:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:24:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:24:12] Found vcfuniq - /usr/local/bin/vcfuniq
[01:24:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:24:12] Found gzip - /bin/gzip
[01:24:12] Found vt - /usr/local/bin/vt
[01:24:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:24:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:24:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:24:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:24:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:24:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:24:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:24:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:25:18] This is snippy 4.6.0Show full stderr[01:25:18] This is snippy 4.6.0
[01:25:18] Written by Torsten Seemann
[01:25:18] Obtained from https://github.com/tseemann/snippy
[01:25:18] Detected operating system: linux
[01:25:18] Enabling bundled linux tools.
[01:25:18] Found bwa - /usr/local/bin/bwa
[01:25:18] Found bcftools - /usr/local/bin/bcftools
[01:25:18] Found samtools - /usr/local/bin/samtools
[01:25:18] Found java - /usr/local/bin/java
[01:25:18] Found snpEff - /usr/local/bin/snpEff
[01:25:18] Found samclip - /usr/local/bin/samclip
[01:25:18] Found seqtk - /usr/local/bin/seqtk
[01:25:18] Found parallel - /usr/local/bin/parallel
[01:25:18] Found freebayes - /usr/local/bin/freebayes
[01:25:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:25:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:25:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:25:18] Found vcfuniq - /usr/local/bin/vcfuniq
[01:25:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:25:18] Found gzip - /bin/gzip
[01:25:19] Found vt - /usr/local/bin/vt
[01:25:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:25:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:25:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:25:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:25:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:25:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:25:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:25:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:57:38] This is snippy 4.6.0Show full stderr[01:57:38] This is snippy 4.6.0
[01:57:38] Written by Torsten Seemann
[01:57:38] Obtained from https://github.com/tseemann/snippy
[01:57:38] Detected operating system: linux
[01:57:38] Enabling bundled linux tools.
[01:57:38] Found bwa - /usr/local/bin/bwa
[01:57:38] Found bcftools - /usr/local/bin/bcftools
[01:57:38] Found samtools - /usr/local/bin/samtools
[01:57:38] Found java - /usr/local/bin/java
[01:57:38] Found snpEff - /usr/local/bin/snpEff
[01:57:38] Found samclip - /usr/local/bin/samclip
[01:57:38] Found seqtk - /usr/local/bin/seqtk
[01:57:38] Found parallel - /usr/local/bin/parallel
[01:57:38] Found freebayes - /usr/local/bin/freebayes
[01:57:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:57:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:57:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:57:38] Found vcfuniq - /usr/local/bin/vcfuniq
[01:57:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:57:38] Found gzip - /bin/gzip
[01:57:38] Found vt - /usr/local/bin/vt
[01:57:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:57:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:57:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:57:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:57:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:57:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:57:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:57:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:25:55] This is snippy 4.6.0Show full stderr[01:25:55] This is snippy 4.6.0
[01:25:55] Written by Torsten Seemann
[01:25:55] Obtained from https://github.com/tseemann/snippy
[01:25:55] Detected operating system: linux
[01:25:55] Enabling bundled linux tools.
[01:25:55] Found bwa - /usr/local/bin/bwa
[01:25:55] Found bcftools - /usr/local/bin/bcftools
[01:25:55] Found samtools - /usr/local/bin/samtools
[01:25:55] Found java - /usr/local/bin/java
[01:25:55] Found snpEff - /usr/local/bin/snpEff
[01:25:55] Found samclip - /usr/local/bin/samclip
[01:25:55] Found seqtk - /usr/local/bin/seqtk
[01:25:55] Found parallel - /usr/local/bin/parallel
[01:25:55] Found freebayes - /usr/local/bin/freebayes
[01:25:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:25:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:25:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:25:55] Found vcfuniq - /usr/local/bin/vcfuniq
[01:25:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:25:55] Found gzip - /bin/gzip
[01:25:55] Found vt - /usr/local/bin/vt
[01:25:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:25:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:25:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:25:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:25:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:25:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:25:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:25:57] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:25:51] This is snippy 4.6.0Show full stderr[01:25:51] This is snippy 4.6.0
[01:25:51] Written by Torsten Seemann
[01:25:51] Obtained from https://github.com/tseemann/snippy
[01:25:51] Detected operating system: linux
[01:25:51] Enabling bundled linux tools.
[01:25:51] Found bwa - /usr/local/bin/bwa
[01:25:51] Found bcftools - /usr/local/bin/bcftools
[01:25:51] Found samtools - /usr/local/bin/samtools
[01:25:51] Found java - /usr/local/bin/java
[01:25:51] Found snpEff - /usr/local/bin/snpEff
[01:25:51] Found samclip - /usr/local/bin/samclip
[01:25:51] Found seqtk - /usr/local/bin/seqtk
[01:25:51] Found parallel - /usr/local/bin/parallel
[01:25:51] Found freebayes - /usr/local/bin/freebayes
[01:25:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:25:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:25:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:25:51] Found vcfuniq - /usr/local/bin/vcfuniq
[01:25:51] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:25:51] Found gzip - /bin/gzip
[01:25:51] Found vt - /usr/local/bin/vt
[01:25:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:25:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:25:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:25:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:25:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:25:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:25:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:25:52] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [10:15:43] This is snippy 4.6.0Show full stderr[10:15:43] This is snippy 4.6.0
[10:15:43] Written by Torsten Seemann
[10:15:43] Obtained from https://github.com/tseemann/snippy
[10:15:43] Detected operating system: linux
[10:15:43] Enabling bundled linux tools.
[10:15:43] Found bwa - /usr/local/bin/bwa
[10:15:43] Found bcftools - /usr/local/bin/bcftools
[10:15:43] Found samtools - /usr/local/bin/samtools
[10:15:43] Found java - /usr/local/bin/java
[10:15:43] Found snpEff - /usr/local/bin/snpEff
[10:15:43] Found samclip - /usr/local/bin/samclip
[10:15:43] Found seqtk - /usr/local/bin/seqtk
[10:15:43] Found parallel - /usr/local/bin/parallel
[10:15:43] Found freebayes - /usr/local/bin/freebayes
[10:15:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:15:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:15:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:15:43] Found vcfuniq - /usr/local/bin/vcfuniq
[10:15:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:15:43] Found gzip - /bin/gzip
[10:15:43] Found vt - /usr/local/bin/vt
[10:15:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:15:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:15:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:16:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:16:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:16:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:16:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:16:05] Using reference: /corral4/main/objects/d/7/6/dataset_d764c547-d517-4ce6-9e7c-25fb605e00f7.dat
[10:16:05] Treating reference as 'genbank' format.
[10:16:05] Will use 1 CPU cores.
[10:16:06] Using read file: /corral4/main/objects/c/7/1/dataset_c711a7bd-3ee2-4f67-a5fb-3c76fa60a96f.dat
[10:16:06] Using read file: /corral4/main/objects/6/8/7/dataset_68771818-54a9-4b11-97b5-0a76985f5fd6.dat
[10:16:06] Creating folder: 80012_S96_L001_R1_001_fastq
[10:16:06] Changing working directory: 80012_S96_L001_R1_001_fastq
[10:16:06] Creating reference folder: reference
[10:16:06] Extracting FASTA and GFF from reference.
Use of uninitialized value in uc at /usr/local/bin/snippy line 206, <GEN0> line 89.
[10:16:06] Wrote 1 sequences to ref.fa
[10:16:06] Wrote 0 features to ref.gff
[10:16:06] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[10:16:06] Using BAM RG (Read Group) ID: 80012_S96_L001_R1_001_fastq
[10:16:07] Running: samtools faidx reference/ref.fa 2>> snps.log
[10:16:07] Error running command, check 80012_S96_L001_R1_001_fastq/snps.log |
| 1 | [23:49:37] This is snippy 4.6.0Show full stderr[23:49:37] This is snippy 4.6.0
[23:49:37] Written by Torsten Seemann
[23:49:37] Obtained from https://github.com/tseemann/snippy
[23:49:37] Detected operating system: linux
[23:49:37] Enabling bundled linux tools.
[23:49:37] Found bwa - /usr/local/bin/bwa
[23:49:37] Found bcftools - /usr/local/bin/bcftools
[23:49:37] Found samtools - /usr/local/bin/samtools
[23:49:37] Found java - /usr/local/bin/java
[23:49:37] Found snpEff - /usr/local/bin/snpEff
[23:49:37] Found samclip - /usr/local/bin/samclip
[23:49:37] Found seqtk - /usr/local/bin/seqtk
[23:49:37] Found parallel - /usr/local/bin/parallel
[23:49:37] Found freebayes - /usr/local/bin/freebayes
[23:49:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:49:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:49:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:49:37] Found vcfuniq - /usr/local/bin/vcfuniq
[23:49:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:49:37] Found gzip - /bin/gzip
[23:49:37] Found vt - /usr/local/bin/vt
[23:49:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:49:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:49:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:49:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:49:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:49:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:49:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:49:39] Using reference: /corral4/main/objects/d/7/6/dataset_d764c547-d517-4ce6-9e7c-25fb605e00f7.dat
[23:49:39] Treating reference as 'genbank' format.
[23:49:39] Will use 1 CPU cores.
[23:49:39] Using read file: /corral4/main/objects/c/7/1/dataset_c711a7bd-3ee2-4f67-a5fb-3c76fa60a96f.dat
[23:49:39] Using read file: /corral4/main/objects/6/8/7/dataset_68771818-54a9-4b11-97b5-0a76985f5fd6.dat
[23:49:39] Creating folder: 80012_S96_L001_R1_001_fastq
[23:49:39] Changing working directory: 80012_S96_L001_R1_001_fastq
[23:49:39] Creating reference folder: reference
[23:49:39] Extracting FASTA and GFF from reference.
Use of uninitialized value in uc at /usr/local/bin/snippy line 206, <GEN0> line 89.
[23:49:39] Wrote 1 sequences to ref.fa
[23:49:39] Wrote 0 features to ref.gff
[23:49:39] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[23:49:39] Using BAM RG (Read Group) ID: 80012_S96_L001_R1_001_fastq
[23:49:39] Running: samtools faidx reference/ref.fa 2>> snps.log
[23:49:39] Error running command, check 80012_S96_L001_R1_001_fastq/snps.log |
| 1 | [18:34:22] This is snippy 4.6.0Show full stderr[18:34:22] This is snippy 4.6.0
[18:34:22] Written by Torsten Seemann
[18:34:22] Obtained from https://github.com/tseemann/snippy
[18:34:22] Detected operating system: linux
[18:34:22] Enabling bundled linux tools.
[18:34:22] Found bwa - /usr/local/bin/bwa
[18:34:22] Found bcftools - /usr/local/bin/bcftools
[18:34:22] Found samtools - /usr/local/bin/samtools
[18:34:22] Found java - /usr/local/bin/java
[18:34:22] Found snpEff - /usr/local/bin/snpEff
[18:34:22] Found samclip - /usr/local/bin/samclip
[18:34:22] Found seqtk - /usr/local/bin/seqtk
[18:34:22] Found parallel - /usr/local/bin/parallel
[18:34:22] Found freebayes - /usr/local/bin/freebayes
[18:34:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:34:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:34:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:34:22] Found vcfuniq - /usr/local/bin/vcfuniq
[18:34:22] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:34:22] Found gzip - /bin/gzip
[18:34:22] Found vt - /usr/local/bin/vt
[18:34:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:34:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:34:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:34:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:34:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:34:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:34:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:34:23] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/259/seq/eschColi_EDL933.fa
[18:34:23] Treating reference as 'fasta' format.
[18:34:23] Will use 1 CPU cores.
[18:34:23] Using read file: /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat
[18:34:23] Creating folder: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[18:34:23] Changing working directory: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[18:34:23] Creating reference folder: reference
[18:34:23] Extracting FASTA and GFF from reference.
[18:34:24] Wrote 2 sequences to ref.fa
[18:34:24] Wrote 0 features to ref.gff
[18:34:24] Shredding /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat into pseudo-reads
[18:35:54] Wrote 8662850 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[18:35:54] Freebayes will process 1 chunks of 5714218 bp, 1 chunks at a time.
[18:35:54] Using BAM RG (Read Group) ID: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[18:35:54] Running: samtools faidx reference/ref.fa 2>> snps.log
[18:35:55] Running: bwa index reference/ref.fa 2>> snps.log
[18:35:58] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[18:35:58] Running: ln -sf reference/ref.fa . 2>> snps.log
[18:35:58] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[18:35:58] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[18:35:58] Running: bwa mem -Y -M -R '@RG\tID:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment\tSM:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/951/72951307/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/951/72951307/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/951/72951307/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs |
| 1 | [18:40:26] This is snippy 4.6.0Show full stderr[18:40:26] This is snippy 4.6.0
[18:40:26] Written by Torsten Seemann
[18:40:26] Obtained from https://github.com/tseemann/snippy
[18:40:26] Detected operating system: linux
[18:40:26] Enabling bundled linux tools.
[18:40:26] Found bwa - /usr/local/bin/bwa
[18:40:26] Found bcftools - /usr/local/bin/bcftools
[18:40:26] Found samtools - /usr/local/bin/samtools
[18:40:26] Found java - /usr/local/bin/java
[18:40:26] Found snpEff - /usr/local/bin/snpEff
[18:40:26] Found samclip - /usr/local/bin/samclip
[18:40:26] Found seqtk - /usr/local/bin/seqtk
[18:40:26] Found parallel - /usr/local/bin/parallel
[18:40:26] Found freebayes - /usr/local/bin/freebayes
[18:40:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[18:40:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[18:40:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[18:40:26] Found vcfuniq - /usr/local/bin/vcfuniq
[18:40:26] Found vcffirstheader - /usr/local/bin/vcffirstheader
[18:40:26] Found gzip - /bin/gzip
[18:40:26] Found vt - /usr/local/bin/vt
[18:40:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[18:40:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[18:40:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[18:40:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[18:40:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[18:40:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[18:40:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[18:40:27] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/259/seq/eschColi_EDL933.fa
[18:40:27] Treating reference as 'fasta' format.
[18:40:27] Will use 1 CPU cores.
[18:40:27] Using read file: /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat
[18:40:27] Creating folder: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[18:40:27] Changing working directory: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[18:40:27] Creating reference folder: reference
[18:40:27] Extracting FASTA and GFF from reference.
[18:40:27] Wrote 2 sequences to ref.fa
[18:40:27] Wrote 0 features to ref.gff
[18:40:27] Shredding /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat into pseudo-reads
[18:41:54] Wrote 8662850 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[18:41:54] Freebayes will process 1 chunks of 5714218 bp, 1 chunks at a time.
[18:41:54] Using BAM RG (Read Group) ID: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[18:41:54] Running: samtools faidx reference/ref.fa 2>> snps.log
[18:41:54] Running: bwa index reference/ref.fa 2>> snps.log
[18:41:59] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[18:41:59] Running: ln -sf reference/ref.fa . 2>> snps.log
[18:41:59] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[18:41:59] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[18:41:59] Running: bwa mem -Y -M -R '@RG\tID:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment\tSM:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/951/72951382/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/951/72951382/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/951/72951382/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs |
| 1 | [19:13:52] This is snippy 4.6.0Show full stderr[19:13:52] This is snippy 4.6.0
[19:13:52] Written by Torsten Seemann
[19:13:52] Obtained from https://github.com/tseemann/snippy
[19:13:52] Detected operating system: linux
[19:13:52] Enabling bundled linux tools.
[19:13:52] Found bwa - /usr/local/bin/bwa
[19:13:52] Found bcftools - /usr/local/bin/bcftools
[19:13:52] Found samtools - /usr/local/bin/samtools
[19:13:52] Found java - /usr/local/bin/java
[19:13:52] Found snpEff - /usr/local/bin/snpEff
[19:13:52] Found samclip - /usr/local/bin/samclip
[19:13:52] Found seqtk - /usr/local/bin/seqtk
[19:13:52] Found parallel - /usr/local/bin/parallel
[19:13:52] Found freebayes - /usr/local/bin/freebayes
[19:13:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:13:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:13:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:13:52] Found vcfuniq - /usr/local/bin/vcfuniq
[19:13:52] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:13:52] Found gzip - /bin/gzip
[19:13:52] Found vt - /usr/local/bin/vt
[19:13:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:13:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:13:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:13:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:13:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:13:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:13:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:13:54] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/259/seq/eschColi_EDL933.fa
[19:13:54] Treating reference as 'fasta' format.
[19:13:54] Will use 1 CPU cores.
[19:13:54] Using read file: /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat
[19:13:54] Creating folder: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[19:13:54] Changing working directory: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[19:13:54] Creating reference folder: reference
[19:13:54] Extracting FASTA and GFF from reference.
[19:13:54] Wrote 2 sequences to ref.fa
[19:13:54] Wrote 0 features to ref.gff
[19:13:54] Shredding /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat into pseudo-reads
[19:15:21] Wrote 8662850 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[19:15:21] Freebayes will process 1 chunks of 5714218 bp, 1 chunks at a time.
[19:15:21] Using BAM RG (Read Group) ID: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[19:15:21] Running: samtools faidx reference/ref.fa 2>> snps.log
[19:15:21] Running: bwa index reference/ref.fa 2>> snps.log
[19:15:26] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[19:15:27] Running: ln -sf reference/ref.fa . 2>> snps.log
[19:15:27] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[19:15:27] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[19:15:27] Running: bwa mem -Y -M -R '@RG\tID:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment\tSM:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/951/72951996/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/951/72951996/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/951/72951996/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs |
| 1 | [19:21:23] This is snippy 4.6.0Show full stderr[19:21:23] This is snippy 4.6.0
[19:21:23] Written by Torsten Seemann
[19:21:23] Obtained from https://github.com/tseemann/snippy
[19:21:23] Detected operating system: linux
[19:21:23] Enabling bundled linux tools.
[19:21:23] Found bwa - /usr/local/bin/bwa
[19:21:23] Found bcftools - /usr/local/bin/bcftools
[19:21:23] Found samtools - /usr/local/bin/samtools
[19:21:23] Found java - /usr/local/bin/java
[19:21:23] Found snpEff - /usr/local/bin/snpEff
[19:21:23] Found samclip - /usr/local/bin/samclip
[19:21:23] Found seqtk - /usr/local/bin/seqtk
[19:21:23] Found parallel - /usr/local/bin/parallel
[19:21:23] Found freebayes - /usr/local/bin/freebayes
[19:21:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[19:21:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[19:21:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[19:21:23] Found vcfuniq - /usr/local/bin/vcfuniq
[19:21:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[19:21:23] Found gzip - /bin/gzip
[19:21:23] Found vt - /usr/local/bin/vt
[19:21:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[19:21:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[19:21:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[19:21:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[19:21:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[19:21:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[19:21:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[19:21:24] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/259/seq/eschColi_EDL933.fa
[19:21:24] Treating reference as 'fasta' format.
[19:21:24] Will use 1 CPU cores.
[19:21:24] Using read file: /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat
[19:21:24] Creating folder: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[19:21:24] Changing working directory: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[19:21:24] Creating reference folder: reference
[19:21:24] Extracting FASTA and GFF from reference.
[19:21:25] Wrote 2 sequences to ref.fa
[19:21:25] Wrote 0 features to ref.gff
[19:21:25] Shredding /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat into pseudo-reads
[19:22:50] Wrote 8662850 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[19:22:50] Freebayes will process 1 chunks of 5714218 bp, 1 chunks at a time.
[19:22:50] Using BAM RG (Read Group) ID: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[19:22:50] Running: samtools faidx reference/ref.fa 2>> snps.log
[19:22:50] Running: bwa index reference/ref.fa 2>> snps.log
[19:22:55] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[19:22:55] Running: ln -sf reference/ref.fa . 2>> snps.log
[19:22:55] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[19:22:55] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[19:22:55] Running: bwa mem -Y -M -R '@RG\tID:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment\tSM:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/952/72952095/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/952/72952095/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/952/72952095/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs |
| 1 | [20:37:58] This is snippy 4.6.0Show full stderr[20:37:58] This is snippy 4.6.0
[20:37:58] Written by Torsten Seemann
[20:37:58] Obtained from https://github.com/tseemann/snippy
[20:37:58] Detected operating system: linux
[20:37:58] Enabling bundled linux tools.
[20:37:58] Found bwa - /usr/local/bin/bwa
[20:37:58] Found bcftools - /usr/local/bin/bcftools
[20:37:58] Found samtools - /usr/local/bin/samtools
[20:37:58] Found java - /usr/local/bin/java
[20:37:58] Found snpEff - /usr/local/bin/snpEff
[20:37:58] Found samclip - /usr/local/bin/samclip
[20:37:58] Found seqtk - /usr/local/bin/seqtk
[20:37:58] Found parallel - /usr/local/bin/parallel
[20:37:58] Found freebayes - /usr/local/bin/freebayes
[20:37:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[20:37:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[20:37:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[20:37:58] Found vcfuniq - /usr/local/bin/vcfuniq
[20:37:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[20:37:58] Found gzip - /bin/gzip
[20:37:58] Found vt - /usr/local/bin/vt
[20:37:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[20:37:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[20:37:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[20:37:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[20:37:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[20:37:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[20:37:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[20:37:59] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/259/seq/eschColi_EDL933.fa
[20:37:59] Treating reference as 'fasta' format.
[20:37:59] Will use 1 CPU cores.
[20:37:59] Using read file: /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat
[20:37:59] Creating folder: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[20:37:59] Changing working directory: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[20:37:59] Creating reference folder: reference
[20:37:59] Extracting FASTA and GFF from reference.
[20:37:59] Wrote 2 sequences to ref.fa
[20:37:59] Wrote 0 features to ref.gff
[20:37:59] Shredding /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat into pseudo-reads
[20:39:29] Wrote 8662850 fake 250bp reads (20x, stride 25bp) to fake_reads.fq
[20:39:29] Freebayes will process 1 chunks of 5714218 bp, 1 chunks at a time.
[20:39:29] Using BAM RG (Read Group) ID: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment
[20:39:29] Running: samtools faidx reference/ref.fa 2>> snps.log
[20:39:30] Running: bwa index reference/ref.fa 2>> snps.log
[20:39:35] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[20:39:35] Running: ln -sf reference/ref.fa . 2>> snps.log
[20:39:35] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[20:39:35] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[20:39:35] Running: bwa mem -Y -M -R '@RG\tID:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment\tSM:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/953/72953104/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/953/72953104/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/953/72953104/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs |
| 1 | [10:36:35] This is snippy 4.6.0Show full stderr[10:36:35] This is snippy 4.6.0
[10:36:35] Written by Torsten Seemann
[10:36:35] Obtained from https://github.com/tseemann/snippy
[10:36:35] Detected operating system: linux
[10:36:35] Enabling bundled linux tools.
[10:36:35] Found bwa - /usr/local/bin/bwa
[10:36:35] Found bcftools - /usr/local/bin/bcftools
[10:36:35] Found samtools - /usr/local/bin/samtools
[10:36:35] Found java - /usr/local/bin/java
[10:36:35] Found snpEff - /usr/local/bin/snpEff
[10:36:35] Found samclip - /usr/local/bin/samclip
[10:36:35] Found seqtk - /usr/local/bin/seqtk
[10:36:35] Found parallel - /usr/local/bin/parallel
[10:36:35] Found freebayes - /usr/local/bin/freebayes
[10:36:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:36:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:36:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:36:35] Found vcfuniq - /usr/local/bin/vcfuniq
[10:36:35] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:36:35] Found gzip - /bin/gzip
[10:36:35] Found vt - /usr/local/bin/vt
[10:36:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:36:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:36:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:36:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:36:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:36:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:36:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:36:36] Using reference: /corral4/main/objects/a/e/9/dataset_ae9a2554-5d57-4553-ade6-30f5f7661efb.dat
[10:36:36] Treating reference as 'genbank' format.
[10:36:36] Will use 1 CPU cores.
[10:36:36] Using read file: /corral4/main/objects/a/0/c/dataset_a0cf1cb7-6df7-4707-83f4-1818a17e2077.dat
[10:36:36] Using read file: /corral4/main/objects/b/c/3/dataset_bc3e9a48-3624-4dbc-bae0-7446ba54eae1.dat
[10:36:36] Creating folder: SRR10761128
[10:36:36] Changing working directory: SRR10761128
[10:36:36] Creating reference folder: reference
[10:36:36] Extracting FASTA and GFF from reference.
[10:36:39] Wrote 1 sequences to ref.fa
[10:36:39] Wrote 4497 features to ref.gff
[10:36:39] Creating reference/snpeff.config
[10:36:39] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[10:36:39] Using BAM RG (Read Group) ID: SRR10761128
[10:36:39] Running: samtools faidx reference/ref.fa 2>> snps.log
[10:36:39] Error running command, check SRR10761128/snps.log |
| 1 | [10:39:03] This is snippy 4.6.0Show full stderr[10:39:03] This is snippy 4.6.0
[10:39:03] Written by Torsten Seemann
[10:39:03] Obtained from https://github.com/tseemann/snippy
[10:39:03] Detected operating system: linux
[10:39:03] Enabling bundled linux tools.
[10:39:03] Found bwa - /usr/local/bin/bwa
[10:39:03] Found bcftools - /usr/local/bin/bcftools
[10:39:03] Found samtools - /usr/local/bin/samtools
[10:39:03] Found java - /usr/local/bin/java
[10:39:03] Found snpEff - /usr/local/bin/snpEff
[10:39:03] Found samclip - /usr/local/bin/samclip
[10:39:03] Found seqtk - /usr/local/bin/seqtk
[10:39:03] Found parallel - /usr/local/bin/parallel
[10:39:03] Found freebayes - /usr/local/bin/freebayes
[10:39:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:39:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:39:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:39:04] Found vcfuniq - /usr/local/bin/vcfuniq
[10:39:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:39:04] Found gzip - /bin/gzip
[10:39:04] Found vt - /usr/local/bin/vt
[10:39:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:39:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:39:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:39:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:39:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:39:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:39:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:39:04] Using reference: /corral4/main/objects/a/e/9/dataset_ae9a2554-5d57-4553-ade6-30f5f7661efb.dat
[10:39:05] Treating reference as 'genbank' format.
[10:39:05] Will use 1 CPU cores.
[10:39:05] Using read file: /corral4/main/objects/e/b/c/dataset_ebcda2c4-64a4-4237-99cd-cc85eef2d369.dat
[10:39:05] Using read file: /corral4/main/objects/d/f/f/dataset_dffb6778-0efb-4c92-be32-92f376eb578a.dat
[10:39:05] Creating folder: SRR10761127
[10:39:05] Changing working directory: SRR10761127
[10:39:05] Creating reference folder: reference
[10:39:05] Extracting FASTA and GFF from reference.
[10:39:07] Wrote 1 sequences to ref.fa
[10:39:07] Wrote 4497 features to ref.gff
[10:39:07] Creating reference/snpeff.config
[10:39:07] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[10:39:07] Using BAM RG (Read Group) ID: SRR10761127
[10:39:07] Running: samtools faidx reference/ref.fa 2>> snps.log
[10:39:07] Error running command, check SRR10761127/snps.log |
| 1 | [10:40:54] This is snippy 4.6.0Show full stderr[10:40:54] This is snippy 4.6.0
[10:40:54] Written by Torsten Seemann
[10:40:54] Obtained from https://github.com/tseemann/snippy
[10:40:54] Detected operating system: linux
[10:40:54] Enabling bundled linux tools.
[10:40:54] Found bwa - /usr/local/bin/bwa
[10:40:54] Found bcftools - /usr/local/bin/bcftools
[10:40:55] Found samtools - /usr/local/bin/samtools
[10:40:55] Found java - /usr/local/bin/java
[10:40:55] Found snpEff - /usr/local/bin/snpEff
[10:40:55] Found samclip - /usr/local/bin/samclip
[10:40:55] Found seqtk - /usr/local/bin/seqtk
[10:40:55] Found parallel - /usr/local/bin/parallel
[10:40:55] Found freebayes - /usr/local/bin/freebayes
[10:40:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:40:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:40:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:40:55] Found vcfuniq - /usr/local/bin/vcfuniq
[10:40:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:40:55] Found gzip - /bin/gzip
[10:40:55] Found vt - /usr/local/bin/vt
[10:40:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:40:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:40:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:40:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:40:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:40:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:40:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:40:55] Using reference: /corral4/main/objects/a/e/9/dataset_ae9a2554-5d57-4553-ade6-30f5f7661efb.dat
[10:40:56] Treating reference as 'genbank' format.
[10:40:56] Will use 1 CPU cores.
[10:40:56] Using read file: /corral4/main/objects/c/5/6/dataset_c56e56b0-69e2-4905-bb28-d1a0854f51e4.dat
[10:40:56] Using read file: /corral4/main/objects/9/2/2/dataset_922c6e30-956d-4c2d-bc51-8cc2d5668c34.dat
[10:40:56] Creating folder: SRR10761126
[10:40:56] Changing working directory: SRR10761126
[10:40:56] Creating reference folder: reference
[10:40:56] Extracting FASTA and GFF from reference.
[10:40:58] Wrote 1 sequences to ref.fa
[10:40:58] Wrote 4497 features to ref.gff
[10:40:58] Creating reference/snpeff.config
[10:40:58] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[10:40:58] Using BAM RG (Read Group) ID: SRR10761126
[10:40:58] Running: samtools faidx reference/ref.fa 2>> snps.log
[10:40:58] Error running command, check SRR10761126/snps.log |
| 1 | [10:50:21] This is snippy 4.6.0Show full stderr[10:50:21] This is snippy 4.6.0
[10:50:21] Written by Torsten Seemann
[10:50:21] Obtained from https://github.com/tseemann/snippy
[10:50:21] Detected operating system: linux
[10:50:21] Enabling bundled linux tools.
[10:50:21] Found bwa - /usr/local/bin/bwa
[10:50:21] Found bcftools - /usr/local/bin/bcftools
[10:50:21] Found samtools - /usr/local/bin/samtools
[10:50:21] Found java - /usr/local/bin/java
[10:50:21] Found snpEff - /usr/local/bin/snpEff
[10:50:21] Found samclip - /usr/local/bin/samclip
[10:50:21] Found seqtk - /usr/local/bin/seqtk
[10:50:21] Found parallel - /usr/local/bin/parallel
[10:50:21] Found freebayes - /usr/local/bin/freebayes
[10:50:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:50:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:50:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:50:21] Found vcfuniq - /usr/local/bin/vcfuniq
[10:50:21] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:50:21] Found gzip - /bin/gzip
[10:50:21] Found vt - /usr/local/bin/vt
[10:50:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:50:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:50:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:50:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:50:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:50:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:50:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:50:22] Using reference: /corral4/main/objects/a/e/9/dataset_ae9a2554-5d57-4553-ade6-30f5f7661efb.dat
[10:50:22] Treating reference as 'genbank' format.
[10:50:22] Will use 1 CPU cores.
[10:50:22] Using read file: /corral4/main/objects/c/5/6/dataset_c56e56b0-69e2-4905-bb28-d1a0854f51e4.dat
[10:50:22] Using read file: /corral4/main/objects/9/2/2/dataset_922c6e30-956d-4c2d-bc51-8cc2d5668c34.dat
[10:50:22] Creating folder: SRR10761126_forward
[10:50:22] Changing working directory: SRR10761126_forward
[10:50:22] Creating reference folder: reference
[10:50:22] Extracting FASTA and GFF from reference.
[10:50:24] Wrote 1 sequences to ref.fa
[10:50:24] Wrote 4497 features to ref.gff
[10:50:24] Creating reference/snpeff.config
[10:50:24] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[10:50:24] Using BAM RG (Read Group) ID: SRR10761126_forward
[10:50:25] Running: samtools faidx reference/ref.fa 2>> snps.log
[10:50:25] Error running command, check SRR10761126_forward/snps.log |
| 1 | [05:01:54] This is snippy 4.6.0Show full stderr[05:01:54] This is snippy 4.6.0
[05:01:54] Written by Torsten Seemann
[05:01:54] Obtained from https://github.com/tseemann/snippy
[05:01:54] Detected operating system: linux
[05:01:54] Enabling bundled linux tools.
[05:01:54] Found bwa - /usr/local/bin/bwa
[05:01:54] Found bcftools - /usr/local/bin/bcftools
[05:01:54] Found samtools - /usr/local/bin/samtools
[05:01:54] Found java - /usr/local/bin/java
[05:01:54] Found snpEff - /usr/local/bin/snpEff
[05:01:54] Found samclip - /usr/local/bin/samclip
[05:01:54] Found seqtk - /usr/local/bin/seqtk
[05:01:54] Found parallel - /usr/local/bin/parallel
[05:01:54] Found freebayes - /usr/local/bin/freebayes
[05:01:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:01:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:01:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:01:54] Found vcfuniq - /usr/local/bin/vcfuniq
[05:01:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:01:54] Found gzip - /bin/gzip
[05:01:54] Found vt - /usr/local/bin/vt
[05:01:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:01:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:01:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:01:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:01:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:01:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:01:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:01:58] Using reference: /corral4/main/objects/7/5/7/dataset_7577fd1d-8b44-4cce-a677-6380b78479e2.dat
[05:01:58] Treating reference as 'fasta' format.
[05:01:58] Will use 1 CPU cores.
[05:01:58] Using read file: /corral4/main/objects/8/c/2/dataset_8c2be7c9-ec84-4b97-9200-90b4f1ca87cb.dat
[05:01:58] Using read file: /corral4/main/objects/4/e/8/dataset_4e87b4ce-e697-4bfd-acd0-b02bfb0ac039.dat
[05:01:58] Creating folder: S7_R1_fastq_gz
[05:01:58] Changing working directory: S7_R1_fastq_gz
[05:01:58] Creating reference folder: reference
[05:01:58] Extracting FASTA and GFF from reference.
[05:01:58] Wrote 15 sequences to ref.fa
[05:01:58] Wrote 0 features to ref.gff
[05:01:58] Freebayes will process 1 chunks of 12573413 bp, 1 chunks at a time.
[05:01:58] Using BAM RG (Read Group) ID: S7_R1_fastq_gz
[05:01:58] Running: samtools faidx reference/ref.fa 2>> snps.log
[05:01:59] Running: bwa index reference/ref.fa 2>> snps.log
[05:02:08] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[05:02:08] Running: ln -sf reference/ref.fa . 2>> snps.log
[05:02:08] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[05:02:08] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[05:02:08] Running: bwa mem -Y -M -R '@RG\tID:S7_R1_fastq_gz\tSM:S7_R1_fastq_gz' -t 1 reference/ref.fa /corral4/main/objects/8/c/2/dataset_8c2be7c9-ec84-4b97-9200-90b4f1ca87cb.dat /corral4/main/objects/4/e/8/dataset_4e87b4ce-e697-4bfd-acd0-b02bfb0ac039.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/010/73010224/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/010/73010224/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/010/73010224/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 15 sequences in reference/ |
| 1 | [08:54:49] This is snippy 4.6.0Show full stderr[08:54:49] This is snippy 4.6.0
[08:54:49] Written by Torsten Seemann
[08:54:49] Obtained from https://github.com/tseemann/snippy
[08:54:49] Detected operating system: linux
[08:54:49] Enabling bundled linux tools.
[08:54:49] Found bwa - /usr/local/bin/bwa
[08:54:49] Found bcftools - /usr/local/bin/bcftools
[08:54:49] Found samtools - /usr/local/bin/samtools
[08:54:49] Found java - /usr/local/bin/java
[08:54:49] Found snpEff - /usr/local/bin/snpEff
[08:54:49] Found samclip - /usr/local/bin/samclip
[08:54:49] Found seqtk - /usr/local/bin/seqtk
[08:54:49] Found parallel - /usr/local/bin/parallel
[08:54:49] Found freebayes - /usr/local/bin/freebayes
[08:54:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:54:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:54:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:54:49] Found vcfuniq - /usr/local/bin/vcfuniq
[08:54:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:54:49] Found gzip - /bin/gzip
[08:54:49] Found vt - /usr/local/bin/vt
[08:54:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:54:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:54:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:54:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:54:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:54:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:54:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:54:50] Using reference: /corral4/main/objects/6/7/d/dataset_67dc2d8d-ac2c-40ad-98bd-47ceff4d01ae.dat
[08:54:50] Treating reference as 'genbank' format.
[08:54:50] Will use 1 CPU cores.
[08:54:50] Using read file: /corral4/main/objects/d/8/e/dataset_d8ebdec0-6eff-408f-be70-4806857fadcf.dat
[08:54:50] Creating folder: PAK_resistant_Strain_zip
[08:54:50] Changing working directory: PAK_resistant_Strain_zip
[08:54:50] Creating reference folder: reference
[08:54:50] Extracting FASTA and GFF from reference.
[08:54:53] Wrote 1 sequences to ref.fa
[08:54:53] Wrote 5867 features to ref.gff
[08:54:53] Creating reference/snpeff.config
[08:54:53] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:54:53] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:54:53] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:54:53] Running: bwa index reference/ref.fa 2>> snps.log
[08:54:57] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[08:54:58] Running: ln -sf reference/ref.fa . 2>> snps.log
[08:54:58] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[08:54:58] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[08:54:58] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[08:55:04] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/d/8/e/dataset_d8ebdec0-6eff-408f-be70-4806857fadcf.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013861/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013861/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013861/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences |
| 1 | [08:54:58] This is snippy 4.6.0Show full stderr[08:54:58] This is snippy 4.6.0
[08:54:58] Written by Torsten Seemann
[08:54:58] Obtained from https://github.com/tseemann/snippy
[08:54:58] Detected operating system: linux
[08:54:58] Enabling bundled linux tools.
[08:54:58] Found bwa - /usr/local/bin/bwa
[08:54:58] Found bcftools - /usr/local/bin/bcftools
[08:54:58] Found samtools - /usr/local/bin/samtools
[08:54:58] Found java - /usr/local/bin/java
[08:54:58] Found snpEff - /usr/local/bin/snpEff
[08:54:58] Found samclip - /usr/local/bin/samclip
[08:54:58] Found seqtk - /usr/local/bin/seqtk
[08:54:58] Found parallel - /usr/local/bin/parallel
[08:54:58] Found freebayes - /usr/local/bin/freebayes
[08:54:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:54:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:54:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:54:58] Found vcfuniq - /usr/local/bin/vcfuniq
[08:54:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:54:58] Found gzip - /bin/gzip
[08:54:58] Found vt - /usr/local/bin/vt
[08:54:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:54:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:54:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:54:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:54:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:54:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:54:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:54:59] Using reference: /corral4/main/objects/c/c/c/dataset_ccc76921-13cc-409b-ab75-a966e36a5169.dat
[08:54:59] Treating reference as 'genbank' format.
[08:54:59] Will use 1 CPU cores.
[08:54:59] Using read file: /corral4/main/objects/a/e/0/dataset_ae0fae57-731f-4dbf-9965-c646cbb4af08.dat
[08:54:59] Creating folder: PAK_resistant_Strain_zip
[08:54:59] Changing working directory: PAK_resistant_Strain_zip
[08:54:59] Creating reference folder: reference
[08:54:59] Extracting FASTA and GFF from reference.
[08:55:02] Wrote 1 sequences to ref.fa
[08:55:02] Wrote 5867 features to ref.gff
[08:55:02] Creating reference/snpeff.config
[08:55:02] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:55:02] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:55:02] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:55:02] Running: bwa index reference/ref.fa 2>> snps.log
[08:55:06] Error running command, check PAK_resistant_Strain_zip/snps.log |
| 1 | [08:55:10] This is snippy 4.6.0Show full stderr[08:55:10] This is snippy 4.6.0
[08:55:10] Written by Torsten Seemann
[08:55:10] Obtained from https://github.com/tseemann/snippy
[08:55:10] Detected operating system: linux
[08:55:10] Enabling bundled linux tools.
[08:55:10] Found bwa - /usr/local/bin/bwa
[08:55:10] Found bcftools - /usr/local/bin/bcftools
[08:55:10] Found samtools - /usr/local/bin/samtools
[08:55:10] Found java - /usr/local/bin/java
[08:55:10] Found snpEff - /usr/local/bin/snpEff
[08:55:10] Found samclip - /usr/local/bin/samclip
[08:55:10] Found seqtk - /usr/local/bin/seqtk
[08:55:10] Found parallel - /usr/local/bin/parallel
[08:55:10] Found freebayes - /usr/local/bin/freebayes
[08:55:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:55:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:55:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:55:11] Found vcfuniq - /usr/local/bin/vcfuniq
[08:55:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:55:11] Found gzip - /bin/gzip
[08:55:11] Found vt - /usr/local/bin/vt
[08:55:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:55:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:55:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:55:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:55:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:55:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:55:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:55:12] Using reference: /corral4/main/objects/7/f/1/dataset_7f1bab6e-e981-4cc0-bed7-4a7086b7b340.dat
[08:55:14] Treating reference as 'genbank' format.
[08:55:14] Will use 1 CPU cores.
[08:55:15] Using read file: /corral4/main/objects/f/b/a/dataset_fbac96ca-2c12-45fd-b918-1f649020b6af.dat
[08:55:15] Creating folder: PAK_resistant_Strain_zip
[08:55:15] Changing working directory: PAK_resistant_Strain_zip
[08:55:15] Creating reference folder: reference
[08:55:15] Extracting FASTA and GFF from reference.
[08:55:18] Wrote 1 sequences to ref.fa
[08:55:18] Wrote 5867 features to ref.gff
[08:55:18] Creating reference/snpeff.config
[08:55:19] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:55:19] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:55:19] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:55:20] Running: bwa index reference/ref.fa 2>> snps.log
[08:55:28] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[08:55:28] Running: ln -sf reference/ref.fa . 2>> snps.log
[08:55:28] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[08:55:29] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[08:55:30] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[08:55:37] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/f/b/a/dataset_fbac96ca-2c12-45fd-b918-1f649020b6af.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013871/tmp --threads 0 -m 4000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013871/tmp --threads 0 -m 4000M | samtools markdup -T /corral4/main/jobs/073/013/73013871/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences in reference/ref.fa.fai
[M::bwa_idx_load_from_disk |
| 1 | [08:55:03] This is snippy 4.6.0Show full stderr[08:55:03] This is snippy 4.6.0
[08:55:03] Written by Torsten Seemann
[08:55:03] Obtained from https://github.com/tseemann/snippy
[08:55:03] Detected operating system: linux
[08:55:03] Enabling bundled linux tools.
[08:55:04] Found bwa - /usr/local/bin/bwa
[08:55:04] Found bcftools - /usr/local/bin/bcftools
[08:55:04] Found samtools - /usr/local/bin/samtools
[08:55:04] Found java - /usr/local/bin/java
[08:55:04] Found snpEff - /usr/local/bin/snpEff
[08:55:04] Found samclip - /usr/local/bin/samclip
[08:55:04] Found seqtk - /usr/local/bin/seqtk
[08:55:04] Found parallel - /usr/local/bin/parallel
[08:55:04] Found freebayes - /usr/local/bin/freebayes
[08:55:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:55:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:55:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:55:04] Found vcfuniq - /usr/local/bin/vcfuniq
[08:55:04] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:55:04] Found gzip - /bin/gzip
[08:55:04] Found vt - /usr/local/bin/vt
[08:55:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:55:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:55:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:55:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:55:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:55:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:55:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:55:04] Using reference: /corral4/main/objects/4/a/f/dataset_4af21818-52fd-41ed-b756-3780f3f34fd3.dat
[08:55:04] Treating reference as 'genbank' format.
[08:55:04] Will use 1 CPU cores.
[08:55:05] Using read file: /corral4/main/objects/3/1/3/dataset_3133fc9f-f54e-447d-8f0e-2b980a1bc605.dat
[08:55:05] Creating folder: PAK_resistant_Strain_zip
[08:55:05] Changing working directory: PAK_resistant_Strain_zip
[08:55:05] Creating reference folder: reference
[08:55:05] Extracting FASTA and GFF from reference.
[08:55:08] Wrote 1 sequences to ref.fa
[08:55:08] Wrote 5867 features to ref.gff
[08:55:08] Creating reference/snpeff.config
[08:55:08] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[08:55:08] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:55:08] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:55:08] Error running command, check PAK_resistant_Strain_zip/snps.log |
| 1 | [08:55:07] This is snippy 4.6.0Show full stderr[08:55:07] This is snippy 4.6.0
[08:55:07] Written by Torsten Seemann
[08:55:07] Obtained from https://github.com/tseemann/snippy
[08:55:07] Detected operating system: linux
[08:55:07] Enabling bundled linux tools.
[08:55:07] Found bwa - /usr/local/bin/bwa
[08:55:07] Found bcftools - /usr/local/bin/bcftools
[08:55:07] Found samtools - /usr/local/bin/samtools
[08:55:07] Found java - /usr/local/bin/java
[08:55:07] Found snpEff - /usr/local/bin/snpEff
[08:55:07] Found samclip - /usr/local/bin/samclip
[08:55:07] Found seqtk - /usr/local/bin/seqtk
[08:55:07] Found parallel - /usr/local/bin/parallel
[08:55:07] Found freebayes - /usr/local/bin/freebayes
[08:55:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:55:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:55:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:55:07] Found vcfuniq - /usr/local/bin/vcfuniq
[08:55:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:55:07] Found gzip - /bin/gzip
[08:55:07] Found vt - /usr/local/bin/vt
[08:55:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:55:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:55:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:55:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:55:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:55:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:55:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:55:07] Using reference: /corral4/main/objects/5/2/1/dataset_52175a55-fab0-4a59-828e-1ca4a8985152.dat
[08:55:08] Treating reference as 'genbank' format.
[08:55:08] Will use 1 CPU cores.
[08:55:08] Using read file: /corral4/main/objects/a/d/b/dataset_adb62186-f480-4f52-b6fd-20b5c72713cd.dat
[08:55:08] Using read file: /corral4/main/objects/a/d/b/dataset_adb62186-f480-4f52-b6fd-20b5c72713cd.dat
[08:55:08] Creating folder: Pseudomonas_aeruginosa_PAK_genomic_fasta
[08:55:08] Changing working directory: Pseudomonas_aeruginosa_PAK_genomic_fasta
[08:55:08] Creating reference folder: reference
[08:55:08] Extracting FASTA and GFF from reference.
[08:55:11] Wrote 1 sequences to ref.fa
[08:55:11] Wrote 5867 features to ref.gff
[08:55:11] Creating reference/snpeff.config
[08:55:11] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:55:11] Using BAM RG (Read Group) ID: Pseudomonas_aeruginosa_PAK_genomic_fasta
[08:55:11] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:55:11] Error running command, check Pseudomonas_aeruginosa_PAK_genomic_fasta/snps.log |
| 1 | [08:55:13] This is snippy 4.6.0Show full stderr[08:55:13] This is snippy 4.6.0
[08:55:13] Written by Torsten Seemann
[08:55:13] Obtained from https://github.com/tseemann/snippy
[08:55:13] Detected operating system: linux
[08:55:13] Enabling bundled linux tools.
[08:55:13] Found bwa - /usr/local/bin/bwa
[08:55:13] Found bcftools - /usr/local/bin/bcftools
[08:55:13] Found samtools - /usr/local/bin/samtools
[08:55:13] Found java - /usr/local/bin/java
[08:55:13] Found snpEff - /usr/local/bin/snpEff
[08:55:13] Found samclip - /usr/local/bin/samclip
[08:55:13] Found seqtk - /usr/local/bin/seqtk
[08:55:13] Found parallel - /usr/local/bin/parallel
[08:55:13] Found freebayes - /usr/local/bin/freebayes
[08:55:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:55:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:55:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:55:14] Found vcfuniq - /usr/local/bin/vcfuniq
[08:55:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:55:14] Found gzip - /bin/gzip
[08:55:14] Found vt - /usr/local/bin/vt
[08:55:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:55:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:55:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:55:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:55:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:55:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:55:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:55:15] Using reference: /corral4/main/objects/8/2/d/dataset_82d0c8e3-2375-41f8-859c-34b1990f6893.dat
[08:55:18] Treating reference as 'genbank' format.
[08:55:18] Will use 1 CPU cores.
[08:55:18] Using read file: /corral4/main/objects/f/0/8/dataset_f0833e1f-e880-4a4f-83dc-b658e7b8831a.dat
[08:55:18] --tmpdir '/corral4/main/jobs/073/013/73013875/tmp' is not a directory |
| 1 | [08:55:39] This is snippy 4.6.0Show full stderr[08:55:39] This is snippy 4.6.0
[08:55:39] Written by Torsten Seemann
[08:55:39] Obtained from https://github.com/tseemann/snippy
[08:55:39] Detected operating system: linux
[08:55:39] Enabling bundled linux tools.
[08:55:39] Found bwa - /usr/local/bin/bwa
[08:55:39] Found bcftools - /usr/local/bin/bcftools
[08:55:39] Found samtools - /usr/local/bin/samtools
[08:55:39] Found java - /usr/local/bin/java
[08:55:39] Found snpEff - /usr/local/bin/snpEff
[08:55:39] Found samclip - /usr/local/bin/samclip
[08:55:39] Found seqtk - /usr/local/bin/seqtk
[08:55:39] Found parallel - /usr/local/bin/parallel
[08:55:39] Found freebayes - /usr/local/bin/freebayes
[08:55:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:55:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:55:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:55:39] Found vcfuniq - /usr/local/bin/vcfuniq
[08:55:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:55:39] Found gzip - /bin/gzip
[08:55:39] Found vt - /usr/local/bin/vt
[08:55:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:55:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:55:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:55:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:55:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:55:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:55:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:55:39] Using reference: /corral4/main/objects/5/0/5/dataset_505c5c07-39f6-4728-92bc-03c4683bad52.dat
[08:55:40] Treating reference as 'genbank' format.
[08:55:40] Will use 1 CPU cores.
[08:55:40] Using read file: /corral4/main/objects/7/0/5/dataset_7059f343-4fa8-4e05-be77-28232f0efe0a.dat
[08:55:40] Creating folder: PAK_resistant_Strain_zip
[08:55:40] Changing working directory: PAK_resistant_Strain_zip
[08:55:40] Creating reference folder: reference
[08:55:40] Extracting FASTA and GFF from reference.
[08:55:43] Wrote 1 sequences to ref.fa
[08:55:43] Wrote 5867 features to ref.gff
[08:55:43] Creating reference/snpeff.config
[08:55:43] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:55:43] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:55:43] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:55:43] Running: bwa index reference/ref.fa 2>> snps.log
[08:55:47] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[08:55:47] Running: ln -sf reference/ref.fa . 2>> snps.log
[08:55:47] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[08:55:47] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[08:55:47] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[08:55:53] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/7/0/5/dataset_7059f343-4fa8-4e05-be77-28232f0efe0a.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013939/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013939/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013939/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences |
| 1 | [08:55:42] This is snippy 4.6.0Show full stderr[08:55:42] This is snippy 4.6.0
[08:55:42] Written by Torsten Seemann
[08:55:42] Obtained from https://github.com/tseemann/snippy
[08:55:42] Detected operating system: linux
[08:55:42] Enabling bundled linux tools.
[08:55:42] Found bwa - /usr/local/bin/bwa
[08:55:42] Found bcftools - /usr/local/bin/bcftools
[08:55:42] Found samtools - /usr/local/bin/samtools
[08:55:42] Found java - /usr/local/bin/java
[08:55:42] Found snpEff - /usr/local/bin/snpEff
[08:55:42] Found samclip - /usr/local/bin/samclip
[08:55:42] Found seqtk - /usr/local/bin/seqtk
[08:55:42] Found parallel - /usr/local/bin/parallel
[08:55:42] Found freebayes - /usr/local/bin/freebayes
[08:55:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:55:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:55:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:55:42] Found vcfuniq - /usr/local/bin/vcfuniq
[08:55:42] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:55:42] Found gzip - /bin/gzip
[08:55:42] Found vt - /usr/local/bin/vt
[08:55:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:55:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:55:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:55:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:55:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:55:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:55:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:55:42] Using reference: /corral4/main/objects/5/2/1/dataset_52175a55-fab0-4a59-828e-1ca4a8985152.dat
[08:55:42] Treating reference as 'genbank' format.
[08:55:42] Will use 1 CPU cores.
[08:55:42] Using read file: /corral4/main/objects/9/2/c/dataset_92c7369e-749f-48bd-8297-af9ccf3349e9.dat
[08:55:42] Creating folder: PAK_resistant_Strain_zip
[08:55:42] Changing working directory: PAK_resistant_Strain_zip
[08:55:42] Creating reference folder: reference
[08:55:42] Extracting FASTA and GFF from reference.
[08:55:46] Wrote 1 sequences to ref.fa
[08:55:46] Wrote 5867 features to ref.gff
[08:55:46] Creating reference/snpeff.config
[08:55:46] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:55:46] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:55:46] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:55:46] Running: bwa index reference/ref.fa 2>> snps.log
[08:55:50] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[08:55:50] Running: ln -sf reference/ref.fa . 2>> snps.log
[08:55:50] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[08:55:50] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[08:55:50] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[08:55:57] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/9/2/c/dataset_92c7369e-749f-48bd-8297-af9ccf3349e9.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013941/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013941/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013941/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences |
| 1 | [08:55:55] This is snippy 4.6.0Show full stderr[08:55:55] This is snippy 4.6.0
[08:55:55] Written by Torsten Seemann
[08:55:55] Obtained from https://github.com/tseemann/snippy
[08:55:55] Detected operating system: linux
[08:55:55] Enabling bundled linux tools.
[08:55:55] Found bwa - /usr/local/bin/bwa
[08:55:55] Found bcftools - /usr/local/bin/bcftools
[08:55:55] Found samtools - /usr/local/bin/samtools
[08:55:55] Found java - /usr/local/bin/java
[08:55:55] Found snpEff - /usr/local/bin/snpEff
[08:55:55] Found samclip - /usr/local/bin/samclip
[08:55:55] Found seqtk - /usr/local/bin/seqtk
[08:55:55] Found parallel - /usr/local/bin/parallel
[08:55:55] Found freebayes - /usr/local/bin/freebayes
[08:55:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:55:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:55:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:55:55] Found vcfuniq - /usr/local/bin/vcfuniq
[08:55:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:55:55] Found gzip - /bin/gzip
[08:55:55] Found vt - /usr/local/bin/vt
[08:55:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:55:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:55:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:55:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:55:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:55:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:55:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:55:56] Using reference: /corral4/main/objects/7/5/0/dataset_750a1866-e250-4785-864e-3176f0899da8.dat
[08:55:56] Treating reference as 'genbank' format.
[08:55:56] Will use 1 CPU cores.
[08:55:56] Using read file: /corral4/main/objects/0/4/9/dataset_0497b5ba-1d9b-4e33-8e5d-487ce10cf95c.dat
[08:55:56] Creating folder: PAK_resistant_Strain_zip
[08:55:56] Changing working directory: PAK_resistant_Strain_zip
[08:55:56] Creating reference folder: reference
[08:55:56] Extracting FASTA and GFF from reference.
[08:55:59] Wrote 1 sequences to ref.fa
[08:55:59] Wrote 5867 features to ref.gff
[08:55:59] Creating reference/snpeff.config
[08:55:59] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:55:59] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:55:59] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:55:59] Running: bwa index reference/ref.fa 2>> snps.log
[08:56:06] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[08:56:06] Running: ln -sf reference/ref.fa . 2>> snps.log
[08:56:06] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[08:56:06] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[08:56:06] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[08:56:13] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/0/4/9/dataset_0497b5ba-1d9b-4e33-8e5d-487ce10cf95c.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013943/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013943/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013943/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences |
| 1 | [08:56:04] This is snippy 4.6.0Show full stderr[08:56:04] This is snippy 4.6.0
[08:56:04] Written by Torsten Seemann
[08:56:04] Obtained from https://github.com/tseemann/snippy
[08:56:04] Detected operating system: linux
[08:56:04] Enabling bundled linux tools.
[08:56:04] Found bwa - /usr/local/bin/bwa
[08:56:04] Found bcftools - /usr/local/bin/bcftools
[08:56:04] Found samtools - /usr/local/bin/samtools
[08:56:04] Found java - /usr/local/bin/java
[08:56:04] Found snpEff - /usr/local/bin/snpEff
[08:56:04] Found samclip - /usr/local/bin/samclip
[08:56:04] Found seqtk - /usr/local/bin/seqtk
[08:56:05] Found parallel - /usr/local/bin/parallel
[08:56:05] Found freebayes - /usr/local/bin/freebayes
[08:56:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:56:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:56:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:56:05] Found vcfuniq - /usr/local/bin/vcfuniq
[08:56:05] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:56:05] Found gzip - /bin/gzip
[08:56:05] Found vt - /usr/local/bin/vt
[08:56:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:56:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:56:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:56:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:56:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:56:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:56:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:56:06] Using reference: /corral4/main/objects/9/3/b/dataset_93b321fd-b84a-47b8-859b-82f530291683.dat
[08:56:09] Treating reference as 'genbank' format.
[08:56:09] Will use 1 CPU cores.
[08:56:09] Using read file: /corral4/main/objects/c/0/1/dataset_c01b95e9-6e67-4f95-b75e-aae4d0b579d4.dat
[08:56:09] Creating folder: PAK_resistant_Strain_zip
[08:56:09] Changing working directory: PAK_resistant_Strain_zip
[08:56:09] Creating reference folder: reference
[08:56:09] Extracting FASTA and GFF from reference.
[08:56:13] Wrote 1 sequences to ref.fa
[08:56:13] Wrote 5867 features to ref.gff
[08:56:13] Creating reference/snpeff.config
[08:56:13] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:56:13] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:56:13] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:56:14] Running: bwa index reference/ref.fa 2>> snps.log
[08:56:22] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[08:56:22] Running: ln -sf reference/ref.fa . 2>> snps.log
[08:56:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[08:56:23] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[08:56:23] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[08:56:31] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/c/0/1/dataset_c01b95e9-6e67-4f95-b75e-aae4d0b579d4.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013946/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013946/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013946/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences in reference/ref.fa.fai
[M::bwa_idx_load_from_di |
| 1 | [08:56:31] This is snippy 4.6.0Show full stderr[08:56:31] This is snippy 4.6.0
[08:56:31] Written by Torsten Seemann
[08:56:31] Obtained from https://github.com/tseemann/snippy
[08:56:31] Detected operating system: linux
[08:56:31] Enabling bundled linux tools.
[08:56:31] Found bwa - /usr/local/bin/bwa
[08:56:31] Found bcftools - /usr/local/bin/bcftools
[08:56:31] Found samtools - /usr/local/bin/samtools
[08:56:31] Found java - /usr/local/bin/java
[08:56:31] Found snpEff - /usr/local/bin/snpEff
[08:56:31] Found samclip - /usr/local/bin/samclip
[08:56:31] Found seqtk - /usr/local/bin/seqtk
[08:56:31] Found parallel - /usr/local/bin/parallel
[08:56:31] Found freebayes - /usr/local/bin/freebayes
[08:56:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:56:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:56:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:56:31] Found vcfuniq - /usr/local/bin/vcfuniq
[08:56:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:56:31] Found gzip - /bin/gzip
[08:56:31] Found vt - /usr/local/bin/vt
[08:56:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:56:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:56:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:56:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:56:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:56:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:56:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:56:31] Using reference: /corral4/main/objects/c/c/c/dataset_ccc76921-13cc-409b-ab75-a966e36a5169.dat
[08:56:32] Treating reference as 'genbank' format.
[08:56:32] Will use 1 CPU cores.
[08:56:32] Using read file: /corral4/main/objects/a/e/0/dataset_ae0fae57-731f-4dbf-9965-c646cbb4af08.dat
[08:56:32] Creating folder: PAK_resistant_Strain_zip
[08:56:32] Changing working directory: PAK_resistant_Strain_zip
[08:56:32] Creating reference folder: reference
[08:56:32] Extracting FASTA and GFF from reference.
[08:56:35] Wrote 1 sequences to ref.fa
[08:56:35] Wrote 5867 features to ref.gff
[08:56:35] Creating reference/snpeff.config
[08:56:35] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:56:35] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:56:35] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:56:35] Running: bwa index reference/ref.fa 2>> snps.log
[08:56:39] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[08:56:39] Running: ln -sf reference/ref.fa . 2>> snps.log
[08:56:39] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[08:56:39] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[08:56:39] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[08:56:45] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/a/e/0/dataset_ae0fae57-731f-4dbf-9965-c646cbb4af08.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013955/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013955/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013955/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences |
| 1 | [08:56:40] This is snippy 4.6.0Show full stderr[08:56:40] This is snippy 4.6.0
[08:56:40] Written by Torsten Seemann
[08:56:40] Obtained from https://github.com/tseemann/snippy
[08:56:40] Detected operating system: linux
[08:56:40] Enabling bundled linux tools.
[08:56:40] Found bwa - /usr/local/bin/bwa
[08:56:40] Found bcftools - /usr/local/bin/bcftools
[08:56:40] Found samtools - /usr/local/bin/samtools
[08:56:40] Found java - /usr/local/bin/java
[08:56:40] Found snpEff - /usr/local/bin/snpEff
[08:56:40] Found samclip - /usr/local/bin/samclip
[08:56:40] Found seqtk - /usr/local/bin/seqtk
[08:56:40] Found parallel - /usr/local/bin/parallel
[08:56:40] Found freebayes - /usr/local/bin/freebayes
[08:56:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:56:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:56:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:56:40] Found vcfuniq - /usr/local/bin/vcfuniq
[08:56:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:56:40] Found gzip - /bin/gzip
[08:56:40] Found vt - /usr/local/bin/vt
[08:56:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:56:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:56:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:56:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:56:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:56:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:56:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:56:40] Using reference: /corral4/main/objects/8/9/f/dataset_89f708b0-3a33-4393-bb58-3e663bcb13fe.dat
[08:56:41] Treating reference as 'genbank' format.
[08:56:41] Will use 1 CPU cores.
[08:56:41] Using read file: /corral4/main/objects/4/0/e/dataset_40e578c2-e503-4958-95f2-763b8d2f4796.dat
[08:56:41] Creating folder: PAK_resistant_Strain_zip
[08:56:41] Changing working directory: PAK_resistant_Strain_zip
[08:56:41] Creating reference folder: reference
[08:56:41] Extracting FASTA and GFF from reference.
[08:56:44] Wrote 1 sequences to ref.fa
[08:56:44] Wrote 5867 features to ref.gff
[08:56:44] Creating reference/snpeff.config
[08:56:44] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:56:44] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:56:44] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:56:44] Running: bwa index reference/ref.fa 2>> snps.log
[08:56:48] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[08:56:48] Running: ln -sf reference/ref.fa . 2>> snps.log
[08:56:48] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[08:56:48] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[08:56:48] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[08:56:54] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/4/0/e/dataset_40e578c2-e503-4958-95f2-763b8d2f4796.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013963/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013963/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013963/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences |
| 1 | [08:57:55] This is snippy 4.6.0Show full stderr[08:57:55] This is snippy 4.6.0
[08:57:55] Written by Torsten Seemann
[08:57:55] Obtained from https://github.com/tseemann/snippy
[08:57:55] Detected operating system: linux
[08:57:55] Enabling bundled linux tools.
[08:57:55] Found bwa - /usr/local/bin/bwa
[08:57:55] Found bcftools - /usr/local/bin/bcftools
[08:57:55] Found samtools - /usr/local/bin/samtools
[08:57:55] Found java - /usr/local/bin/java
[08:57:55] Found snpEff - /usr/local/bin/snpEff
[08:57:55] Found samclip - /usr/local/bin/samclip
[08:57:55] Found seqtk - /usr/local/bin/seqtk
[08:57:55] Found parallel - /usr/local/bin/parallel
[08:57:55] Found freebayes - /usr/local/bin/freebayes
[08:57:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[08:57:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[08:57:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[08:57:55] Found vcfuniq - /usr/local/bin/vcfuniq
[08:57:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[08:57:55] Found gzip - /bin/gzip
[08:57:55] Found vt - /usr/local/bin/vt
[08:57:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[08:57:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[08:57:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[08:57:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[08:57:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[08:57:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[08:57:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[08:57:56] Using reference: /corral4/main/objects/6/7/d/dataset_67dc2d8d-ac2c-40ad-98bd-47ceff4d01ae.dat
[08:57:56] Treating reference as 'genbank' format.
[08:57:56] Will use 1 CPU cores.
[08:57:56] Using read file: /corral4/main/objects/d/8/e/dataset_d8ebdec0-6eff-408f-be70-4806857fadcf.dat
[08:57:56] Creating folder: PAK_resistant_Strain_zip
[08:57:56] Changing working directory: PAK_resistant_Strain_zip
[08:57:56] Creating reference folder: reference
[08:57:56] Extracting FASTA and GFF from reference.
[08:57:59] Wrote 1 sequences to ref.fa
[08:57:59] Wrote 5867 features to ref.gff
[08:57:59] Creating reference/snpeff.config
[08:57:59] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[08:57:59] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[08:57:59] Running: samtools faidx reference/ref.fa 2>> snps.log
[08:57:59] Running: bwa index reference/ref.fa 2>> snps.log
[08:58:05] Error running command, check PAK_resistant_Strain_zip/snps.log |
| 1 | [09:02:03] This is snippy 4.6.0Show full stderr[09:02:03] This is snippy 4.6.0
[09:02:03] Written by Torsten Seemann
[09:02:03] Obtained from https://github.com/tseemann/snippy
[09:02:03] Detected operating system: linux
[09:02:03] Enabling bundled linux tools.
[09:02:03] Found bwa - /usr/local/bin/bwa
[09:02:03] Found bcftools - /usr/local/bin/bcftools
[09:02:03] Found samtools - /usr/local/bin/samtools
[09:02:03] Found java - /usr/local/bin/java
[09:02:03] Found snpEff - /usr/local/bin/snpEff
[09:02:03] Found samclip - /usr/local/bin/samclip
[09:02:03] Found seqtk - /usr/local/bin/seqtk
[09:02:03] Found parallel - /usr/local/bin/parallel
[09:02:03] Found freebayes - /usr/local/bin/freebayes
[09:02:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:02:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:02:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:02:03] Found vcfuniq - /usr/local/bin/vcfuniq
[09:02:03] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:02:03] Found gzip - /bin/gzip
[09:02:03] Found vt - /usr/local/bin/vt
[09:02:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:02:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:02:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:02:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:02:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:02:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:02:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:02:04] Using reference: /corral4/main/objects/8/9/f/dataset_89f708b0-3a33-4393-bb58-3e663bcb13fe.dat
[09:02:04] Treating reference as 'genbank' format.
[09:02:04] Will use 1 CPU cores.
[09:02:04] Using read file: /corral4/main/objects/4/0/e/dataset_40e578c2-e503-4958-95f2-763b8d2f4796.dat
[09:02:04] Creating folder: PAK_resistant_Strain_zip
[09:02:04] Changing working directory: PAK_resistant_Strain_zip
[09:02:04] Creating reference folder: reference
[09:02:04] Extracting FASTA and GFF from reference.
[09:02:08] Wrote 1 sequences to ref.fa
[09:02:08] Wrote 5867 features to ref.gff
[09:02:08] Creating reference/snpeff.config
[09:02:08] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time.
[09:02:08] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[09:02:08] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:02:08] Running: bwa index reference/ref.fa 2>> snps.log
[09:02:15] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:02:15] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:02:15] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:02:16] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:02:16] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[09:02:23] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/4/0/e/dataset_40e578c2-e503-4958-95f2-763b8d2f4796.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/014/73014267/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/014/73014267/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/014/73014267/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences |
| 1 | [09:02:31] This is snippy 4.6.0Show full stderr[09:02:31] This is snippy 4.6.0
[09:02:31] Written by Torsten Seemann
[09:02:31] Obtained from https://github.com/tseemann/snippy
[09:02:31] Detected operating system: linux
[09:02:31] Enabling bundled linux tools.
[09:02:31] Found bwa - /usr/local/bin/bwa
[09:02:31] Found bcftools - /usr/local/bin/bcftools
[09:02:31] Found samtools - /usr/local/bin/samtools
[09:02:31] Found java - /usr/local/bin/java
[09:02:31] Found snpEff - /usr/local/bin/snpEff
[09:02:31] Found samclip - /usr/local/bin/samclip
[09:02:31] Found seqtk - /usr/local/bin/seqtk
[09:02:31] Found parallel - /usr/local/bin/parallel
[09:02:31] Found freebayes - /usr/local/bin/freebayes
[09:02:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:02:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:02:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:02:31] Found vcfuniq - /usr/local/bin/vcfuniq
[09:02:31] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:02:31] Found gzip - /bin/gzip
[09:02:31] Found vt - /usr/local/bin/vt
[09:02:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:02:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:02:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:02:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:02:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:02:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:02:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:02:32] Using reference: /corral4/main/objects/2/8/b/dataset_28bc974e-ae27-4c84-ba56-8144b48f519d.dat
[09:02:32] Treating reference as 'fasta' format.
[09:02:32] Will use 1 CPU cores.
[09:02:32] Using read file: /corral4/main/objects/0/4/9/dataset_0497b5ba-1d9b-4e33-8e5d-487ce10cf95c.dat
[09:02:32] Creating folder: PAK_resistant_Strain_zip
[09:02:32] Changing working directory: PAK_resistant_Strain_zip
[09:02:32] Creating reference folder: reference
[09:02:32] Extracting FASTA and GFF from reference.
[09:02:32] Wrote 1 sequences to ref.fa
[09:02:32] Wrote 0 features to ref.gff
[09:02:32] Freebayes will process 1 chunks of 6502547 bp, 1 chunks at a time.
[09:02:32] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip
[09:02:32] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:02:32] Running: bwa index reference/ref.fa 2>> snps.log
[09:02:37] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:02:37] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:02:37] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:02:37] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:02:37] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/0/4/9/dataset_0497b5ba-1d9b-4e33-8e5d-487ce10cf95c.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/014/73014271/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/014/73014271/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/014/73014271/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 1 sequences in reference/ref.fa.fai
[M::process] read 67296 sequences (10000219 bp)...
[M::process] read 67246 sequences (10000197 bp)...
[M::mem_process_s |
| 1 | [09:20:35] This is snippy 4.6.0Show full stderr[09:20:35] This is snippy 4.6.0
[09:20:35] Written by Torsten Seemann
[09:20:35] Obtained from https://github.com/tseemann/snippy
[09:20:35] Detected operating system: linux
[09:20:35] Enabling bundled linux tools.
[09:20:35] Found bwa - /usr/local/bin/bwa
[09:20:35] Found bcftools - /usr/local/bin/bcftools
[09:20:35] Found samtools - /usr/local/bin/samtools
[09:20:35] Found java - /usr/local/bin/java
[09:20:35] Found snpEff - /usr/local/bin/snpEff
[09:20:35] Found samclip - /usr/local/bin/samclip
[09:20:35] Found seqtk - /usr/local/bin/seqtk
[09:20:35] Found parallel - /usr/local/bin/parallel
[09:20:35] Found freebayes - /usr/local/bin/freebayes
[09:20:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:20:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:20:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:20:36] Found vcfuniq - /usr/local/bin/vcfuniq
[09:20:36] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:20:36] Found gzip - /bin/gzip
[09:20:36] Found vt - /usr/local/bin/vt
[09:20:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:20:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:20:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:20:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:20:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:20:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:20:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:20:37] Using reference: /corral4/main/objects/3/6/9/dataset_3695ece0-8574-430e-be45-4d83063106f4.dat
[09:20:37] Treating reference as 'genbank' format.
[09:20:37] Will use 1 CPU cores.
[09:20:37] Using read file: /corral4/main/objects/c/2/9/dataset_c29f6af4-20e0-4ae3-bf5e-b07e4f6be1b4.dat
[09:20:37] Creating folder: KPC_42_trim_fastq
[09:20:37] Changing working directory: KPC_42_trim_fastq
[09:20:37] Creating reference folder: reference
[09:20:37] Extracting FASTA and GFF from reference.
[09:20:41] Wrote 4 sequences to ref.fa
[09:20:41] Wrote 5625 features to ref.gff
[09:20:41] Creating reference/snpeff.config
[09:20:41] Freebayes will process 1 chunks of 5745542 bp, 1 chunks at a time.
[09:20:41] Using BAM RG (Read Group) ID: KPC_42_trim_fastq
[09:20:41] Running: samtools faidx reference/ref.fa 2>> snps.log
[09:20:41] Running: bwa index reference/ref.fa 2>> snps.log
[09:20:44] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[09:20:44] Running: ln -sf reference/ref.fa . 2>> snps.log
[09:20:44] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[09:20:44] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[09:20:45] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[09:20:49] Error running command, check KPC_42_trim_fastq/snps.log |
| 1 | tar: pECC231/snps.bam: Cannot close: Disk quota exceededShow full stderrtar: pECC231/snps.bam: Cannot close: Disk quota exceeded
tar: Exiting with failure status due to previous errors |
| 1 | [15:58:00] This is snippy 4.6.0Show full stderr[15:58:00] This is snippy 4.6.0
[15:58:00] Written by Torsten Seemann
[15:58:00] Obtained from https://github.com/tseemann/snippy
[15:58:00] Detected operating system: linux
[15:58:00] Enabling bundled linux tools.
[15:58:00] Found bwa - /usr/local/bin/bwa
[15:58:00] Found bcftools - /usr/local/bin/bcftools
[15:58:00] Found samtools - /usr/local/bin/samtools
[15:58:00] Found java - /usr/local/bin/java
[15:58:00] Found snpEff - /usr/local/bin/snpEff
[15:58:00] Found samclip - /usr/local/bin/samclip
[15:58:00] Found seqtk - /usr/local/bin/seqtk
[15:58:00] Found parallel - /usr/local/bin/parallel
[15:58:00] Found freebayes - /usr/local/bin/freebayes
[15:58:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[15:58:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[15:58:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[15:58:00] Found vcfuniq - /usr/local/bin/vcfuniq
[15:58:00] Found vcffirstheader - /usr/local/bin/vcffirstheader
[15:58:00] Found gzip - /bin/gzip
[15:58:00] Found vt - /usr/local/bin/vt
[15:58:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[15:58:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[15:58:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[15:58:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[15:58:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[15:58:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[15:58:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:58:03] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:56:54] This is snippy 4.6.0Show full stderr[14:56:54] This is snippy 4.6.0
[14:56:54] Written by Torsten Seemann
[14:56:54] Obtained from https://github.com/tseemann/snippy
[14:56:54] Detected operating system: linux
[14:56:54] Enabling bundled linux tools.
[14:56:54] Found bwa - /usr/local/bin/bwa
[14:56:54] Found bcftools - /usr/local/bin/bcftools
[14:56:54] Found samtools - /usr/local/bin/samtools
[14:56:54] Found java - /usr/local/bin/java
[14:56:54] Found snpEff - /usr/local/bin/snpEff
[14:56:54] Found samclip - /usr/local/bin/samclip
[14:56:54] Found seqtk - /usr/local/bin/seqtk
[14:56:54] Found parallel - /usr/local/bin/parallel
[14:56:54] Found freebayes - /usr/local/bin/freebayes
[14:56:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:56:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:56:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:56:54] Found vcfuniq - /usr/local/bin/vcfuniq
[14:56:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:56:54] Found gzip - /bin/gzip
[14:56:54] Found vt - /usr/local/bin/vt
[14:56:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:56:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:56:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:56:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:56:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:56:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:56:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:56:55] Using reference: /corral4/main/objects/a/5/1/dataset_a5160a31-fbb6-42eb-8aa5-a52875760c5c.dat
[14:56:55] Could not guess format '/corral4/main/objects/a/5/1/dataset_a5160a31-fbb6-42eb-8aa5-a52875760c5c.dat' |
| 1 | [17:04:32] This is snippy 4.6.0Show full stderr[17:04:32] This is snippy 4.6.0
[17:04:32] Written by Torsten Seemann
[17:04:32] Obtained from https://github.com/tseemann/snippy
[17:04:32] Detected operating system: linux
[17:04:32] Enabling bundled linux tools.
[17:04:32] Found bwa - /usr/local/bin/bwa
[17:04:32] Found bcftools - /usr/local/bin/bcftools
[17:04:32] Found samtools - /usr/local/bin/samtools
[17:04:32] Found java - /usr/local/bin/java
[17:04:32] Found snpEff - /usr/local/bin/snpEff
[17:04:32] Found samclip - /usr/local/bin/samclip
[17:04:32] Found seqtk - /usr/local/bin/seqtk
[17:04:32] Found parallel - /usr/local/bin/parallel
[17:04:32] Found freebayes - /usr/local/bin/freebayes
[17:04:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[17:04:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[17:04:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[17:04:32] Found vcfuniq - /usr/local/bin/vcfuniq
[17:04:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[17:04:32] Found gzip - /bin/gzip
[17:04:32] Found vt - /usr/local/bin/vt
[17:04:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[17:04:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[17:04:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[17:04:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[17:04:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[17:04:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[17:04:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[17:04:32] Using reference: /jetstream2/scratch/main/jobs/73095304/inputs/dataset_a5160a31-fbb6-42eb-8aa5-a52875760c5c.dat
[17:04:32] Could not guess format '/jetstream2/scratch/main/jobs/73095304/inputs/dataset_a5160a31-fbb6-42eb-8aa5-a52875760c5c.dat' |
| 1 | [23:42:45] This is snippy 4.6.0Show full stderr[23:42:45] This is snippy 4.6.0
[23:42:45] Written by Torsten Seemann
[23:42:45] Obtained from https://github.com/tseemann/snippy
[23:42:45] Detected operating system: linux
[23:42:45] Enabling bundled linux tools.
[23:42:45] Found bwa - /usr/local/bin/bwa
[23:42:45] Found bcftools - /usr/local/bin/bcftools
[23:42:45] Found samtools - /usr/local/bin/samtools
[23:42:45] Found java - /usr/local/bin/java
[23:42:45] Found snpEff - /usr/local/bin/snpEff
[23:42:45] Found samclip - /usr/local/bin/samclip
[23:42:45] Found seqtk - /usr/local/bin/seqtk
[23:42:45] Found parallel - /usr/local/bin/parallel
[23:42:45] Found freebayes - /usr/local/bin/freebayes
[23:42:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:42:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:42:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:42:45] Found vcfuniq - /usr/local/bin/vcfuniq
[23:42:45] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:42:45] Found gzip - /bin/gzip
[23:42:45] Found vt - /usr/local/bin/vt
[23:42:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:42:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:42:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:42:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:42:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:42:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:42:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:42:46] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:45:57] This is snippy 4.6.0Show full stderr[23:45:57] This is snippy 4.6.0
[23:45:57] Written by Torsten Seemann
[23:45:57] Obtained from https://github.com/tseemann/snippy
[23:45:57] Detected operating system: linux
[23:45:57] Enabling bundled linux tools.
[23:45:57] Found bwa - /usr/local/bin/bwa
[23:45:57] Found bcftools - /usr/local/bin/bcftools
[23:45:57] Found samtools - /usr/local/bin/samtools
[23:45:57] Found java - /usr/local/bin/java
[23:45:57] Found snpEff - /usr/local/bin/snpEff
[23:45:57] Found samclip - /usr/local/bin/samclip
[23:45:57] Found seqtk - /usr/local/bin/seqtk
[23:45:57] Found parallel - /usr/local/bin/parallel
[23:45:57] Found freebayes - /usr/local/bin/freebayes
[23:45:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:45:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:45:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:45:57] Found vcfuniq - /usr/local/bin/vcfuniq
[23:45:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:45:57] Found gzip - /bin/gzip
[23:45:57] Found vt - /usr/local/bin/vt
[23:45:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:45:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:45:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:45:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:45:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:45:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:45:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:45:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:02:28] This is snippy 4.6.0Show full stderr[00:02:28] This is snippy 4.6.0
[00:02:28] Written by Torsten Seemann
[00:02:28] Obtained from https://github.com/tseemann/snippy
[00:02:28] Detected operating system: linux
[00:02:28] Enabling bundled linux tools.
[00:02:28] Found bwa - /usr/local/bin/bwa
[00:02:28] Found bcftools - /usr/local/bin/bcftools
[00:02:28] Found samtools - /usr/local/bin/samtools
[00:02:28] Found java - /usr/local/bin/java
[00:02:28] Found snpEff - /usr/local/bin/snpEff
[00:02:28] Found samclip - /usr/local/bin/samclip
[00:02:28] Found seqtk - /usr/local/bin/seqtk
[00:02:29] Found parallel - /usr/local/bin/parallel
[00:02:29] Found freebayes - /usr/local/bin/freebayes
[00:02:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:02:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:02:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:02:29] Found vcfuniq - /usr/local/bin/vcfuniq
[00:02:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:02:29] Found gzip - /bin/gzip
[00:02:29] Found vt - /usr/local/bin/vt
[00:02:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:02:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:02:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:02:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:02:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:02:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:02:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:02:29] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:11:40] This is snippy 4.6.0Show full stderr[07:11:40] This is snippy 4.6.0
[07:11:40] Written by Torsten Seemann
[07:11:40] Obtained from https://github.com/tseemann/snippy
[07:11:40] Detected operating system: linux
[07:11:40] Enabling bundled linux tools.
[07:11:40] Found bwa - /usr/local/bin/bwa
[07:11:40] Found bcftools - /usr/local/bin/bcftools
[07:11:40] Found samtools - /usr/local/bin/samtools
[07:11:40] Found java - /usr/local/bin/java
[07:11:40] Found snpEff - /usr/local/bin/snpEff
[07:11:40] Found samclip - /usr/local/bin/samclip
[07:11:40] Found seqtk - /usr/local/bin/seqtk
[07:11:40] Found parallel - /usr/local/bin/parallel
[07:11:40] Found freebayes - /usr/local/bin/freebayes
[07:11:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:11:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:11:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:11:40] Found vcfuniq - /usr/local/bin/vcfuniq
[07:11:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:11:40] Found gzip - /bin/gzip
[07:11:40] Found vt - /usr/local/bin/vt
[07:11:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:11:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:11:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:11:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:11:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:11:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:11:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:11:42] Using reference: /corral4/main/objects/b/3/5/dataset_b355f287-7d9e-49b8-b0db-adb9b89cf8a2.dat
[07:11:42] Could not guess format '/corral4/main/objects/b/3/5/dataset_b355f287-7d9e-49b8-b0db-adb9b89cf8a2.dat' |
| 1 | [09:17:53] This is snippy 4.6.0Show full stderr[09:17:53] This is snippy 4.6.0
[09:17:53] Written by Torsten Seemann
[09:17:53] Obtained from https://github.com/tseemann/snippy
[09:17:53] Detected operating system: linux
[09:17:53] Enabling bundled linux tools.
[09:17:53] Found bwa - /usr/local/bin/bwa
[09:17:53] Found bcftools - /usr/local/bin/bcftools
[09:17:53] Found samtools - /usr/local/bin/samtools
[09:17:53] Found java - /usr/local/bin/java
[09:17:53] Found snpEff - /usr/local/bin/snpEff
[09:17:53] Found samclip - /usr/local/bin/samclip
[09:17:53] Found seqtk - /usr/local/bin/seqtk
[09:17:53] Found parallel - /usr/local/bin/parallel
[09:17:54] Found freebayes - /usr/local/bin/freebayes
[09:17:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:17:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:17:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:17:54] Found vcfuniq - /usr/local/bin/vcfuniq
[09:17:54] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:17:54] Found gzip - /bin/gzip
[09:17:54] Found vt - /usr/local/bin/vt
[09:17:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:17:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:17:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:17:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:17:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:17:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:17:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:17:55] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [09:21:11] This is snippy 4.6.0Show full stderr[09:21:11] This is snippy 4.6.0
[09:21:11] Written by Torsten Seemann
[09:21:11] Obtained from https://github.com/tseemann/snippy
[09:21:11] Detected operating system: linux
[09:21:11] Enabling bundled linux tools.
[09:21:11] Found bwa - /usr/local/bin/bwa
[09:21:11] Found bcftools - /usr/local/bin/bcftools
[09:21:11] Found samtools - /usr/local/bin/samtools
[09:21:11] Found java - /usr/local/bin/java
[09:21:11] Found snpEff - /usr/local/bin/snpEff
[09:21:11] Found samclip - /usr/local/bin/samclip
[09:21:11] Found seqtk - /usr/local/bin/seqtk
[09:21:11] Found parallel - /usr/local/bin/parallel
[09:21:11] Found freebayes - /usr/local/bin/freebayes
[09:21:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[09:21:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[09:21:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[09:21:11] Found vcfuniq - /usr/local/bin/vcfuniq
[09:21:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[09:21:11] Found gzip - /bin/gzip
[09:21:11] Found vt - /usr/local/bin/vt
[09:21:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[09:21:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[09:21:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[09:21:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[09:21:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[09:21:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[09:21:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[09:21:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [10:47:05] This is snippy 4.6.0Show full stderr[10:47:05] This is snippy 4.6.0
[10:47:05] Written by Torsten Seemann
[10:47:05] Obtained from https://github.com/tseemann/snippy
[10:47:05] Detected operating system: linux
[10:47:05] Enabling bundled linux tools.
[10:47:05] Found bwa - /usr/local/bin/bwa
[10:47:05] Found bcftools - /usr/local/bin/bcftools
[10:47:05] Found samtools - /usr/local/bin/samtools
[10:47:05] Found java - /usr/local/bin/java
[10:47:05] Found snpEff - /usr/local/bin/snpEff
[10:47:05] Found samclip - /usr/local/bin/samclip
[10:47:05] Found seqtk - /usr/local/bin/seqtk
[10:47:05] Found parallel - /usr/local/bin/parallel
[10:47:06] Found freebayes - /usr/local/bin/freebayes
[10:47:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:47:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:47:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:47:06] Found vcfuniq - /usr/local/bin/vcfuniq
[10:47:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:47:06] Found gzip - /bin/gzip
[10:47:06] Found vt - /usr/local/bin/vt
[10:47:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:47:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:47:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:47:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:47:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:47:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:47:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:47:07] Using reference: /corral4/main/objects/7/8/c/dataset_78c04d78-cbdd-48cc-aaf1-b4db1ac78784.dat
[10:47:07] Treating reference as 'genbank' format.
[10:47:07] Will use 1 CPU cores.
[10:47:07] Using read file: /corral4/main/objects/7/7/b/dataset_77b100f5-7e0e-469f-8f2b-80d4094518a1.dat
[10:47:07] Creating folder: SRR36266170_fastq_gz
[10:47:07] Changing working directory: SRR36266170_fastq_gz
[10:47:07] Creating reference folder: reference
[10:47:07] Extracting FASTA and GFF from reference.
[10:47:10] Wrote 1 sequences to ref.fa
[10:47:10] Wrote 4111 features to ref.gff
[10:47:10] Creating reference/snpeff.config
[10:47:10] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[10:47:10] Using BAM RG (Read Group) ID: SRR36266170_fastq_gz
[10:47:10] Running: samtools faidx reference/ref.fa 2>> snps.log
[10:47:10] Error running command, check SRR36266170_fastq_gz/snps.log |
| 1 | [10:54:14] This is snippy 4.6.0Show full stderr[10:54:14] This is snippy 4.6.0
[10:54:14] Written by Torsten Seemann
[10:54:14] Obtained from https://github.com/tseemann/snippy
[10:54:14] Detected operating system: linux
[10:54:14] Enabling bundled linux tools.
[10:54:14] Found bwa - /usr/local/bin/bwa
[10:54:14] Found bcftools - /usr/local/bin/bcftools
[10:54:14] Found samtools - /usr/local/bin/samtools
[10:54:14] Found java - /usr/local/bin/java
[10:54:14] Found snpEff - /usr/local/bin/snpEff
[10:54:14] Found samclip - /usr/local/bin/samclip
[10:54:14] Found seqtk - /usr/local/bin/seqtk
[10:54:14] Found parallel - /usr/local/bin/parallel
[10:54:14] Found freebayes - /usr/local/bin/freebayes
[10:54:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:54:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:54:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:54:14] Found vcfuniq - /usr/local/bin/vcfuniq
[10:54:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:54:14] Found gzip - /bin/gzip
[10:54:14] Found vt - /usr/local/bin/vt
[10:54:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:54:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:54:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:54:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:54:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:54:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:54:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:54:15] Using reference: /corral4/main/objects/b/0/5/dataset_b05b06e7-abfd-45a9-92bf-d943a6cb035c.dat
[10:54:15] Could not guess format '/corral4/main/objects/b/0/5/dataset_b05b06e7-abfd-45a9-92bf-d943a6cb035c.dat' |
| 1 | [10:58:32] This is snippy 4.6.0Show full stderr[10:58:32] This is snippy 4.6.0
[10:58:32] Written by Torsten Seemann
[10:58:32] Obtained from https://github.com/tseemann/snippy
[10:58:32] Detected operating system: linux
[10:58:32] Enabling bundled linux tools.
[10:58:32] Found bwa - /usr/local/bin/bwa
[10:58:32] Found bcftools - /usr/local/bin/bcftools
[10:58:32] Found samtools - /usr/local/bin/samtools
[10:58:32] Found java - /usr/local/bin/java
[10:58:32] Found snpEff - /usr/local/bin/snpEff
[10:58:32] Found samclip - /usr/local/bin/samclip
[10:58:32] Found seqtk - /usr/local/bin/seqtk
[10:58:32] Found parallel - /usr/local/bin/parallel
[10:58:32] Found freebayes - /usr/local/bin/freebayes
[10:58:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[10:58:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[10:58:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[10:58:32] Found vcfuniq - /usr/local/bin/vcfuniq
[10:58:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[10:58:32] Found gzip - /bin/gzip
[10:58:32] Found vt - /usr/local/bin/vt
[10:58:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[10:58:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[10:58:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[10:58:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[10:58:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[10:58:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[10:58:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[10:58:33] Using reference: /corral4/main/objects/b/0/5/dataset_b05b06e7-abfd-45a9-92bf-d943a6cb035c.dat
[10:58:33] Could not guess format '/corral4/main/objects/b/0/5/dataset_b05b06e7-abfd-45a9-92bf-d943a6cb035c.dat' |
| 1 | [22:28:23] This is snippy 4.6.0Show full stderr[22:28:23] This is snippy 4.6.0
[22:28:23] Written by Torsten Seemann
[22:28:23] Obtained from https://github.com/tseemann/snippy
[22:28:23] Detected operating system: linux
[22:28:23] Enabling bundled linux tools.
[22:28:23] Found bwa - /usr/local/bin/bwa
[22:28:23] Found bcftools - /usr/local/bin/bcftools
[22:28:23] Found samtools - /usr/local/bin/samtools
[22:28:23] Found java - /usr/local/bin/java
[22:28:23] Found snpEff - /usr/local/bin/snpEff
[22:28:23] Found samclip - /usr/local/bin/samclip
[22:28:23] Found seqtk - /usr/local/bin/seqtk
[22:28:23] Found parallel - /usr/local/bin/parallel
[22:28:23] Found freebayes - /usr/local/bin/freebayes
[22:28:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:28:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:28:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:28:23] Found vcfuniq - /usr/local/bin/vcfuniq
[22:28:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:28:23] Found gzip - /bin/gzip
[22:28:23] Found vt - /usr/local/bin/vt
[22:28:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:28:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:28:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:28:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:28:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:28:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:28:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:28:24] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [12:27:57] This is snippy 4.6.0Show full stderr[12:27:57] This is snippy 4.6.0
[12:27:57] Written by Torsten Seemann
[12:27:57] Obtained from https://github.com/tseemann/snippy
[12:27:57] Detected operating system: linux
[12:27:57] Enabling bundled linux tools.
[12:27:57] Found bwa - /usr/local/bin/bwa
[12:27:57] Found bcftools - /usr/local/bin/bcftools
[12:27:57] Found samtools - /usr/local/bin/samtools
[12:27:57] Found java - /usr/local/bin/java
[12:27:57] Found snpEff - /usr/local/bin/snpEff
[12:27:57] Found samclip - /usr/local/bin/samclip
[12:27:57] Found seqtk - /usr/local/bin/seqtk
[12:27:57] Found parallel - /usr/local/bin/parallel
[12:27:57] Found freebayes - /usr/local/bin/freebayes
[12:27:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[12:27:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[12:27:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[12:27:57] Found vcfuniq - /usr/local/bin/vcfuniq
[12:27:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[12:27:57] Found gzip - /bin/gzip
[12:27:57] Found vt - /usr/local/bin/vt
[12:27:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[12:27:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[12:27:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[12:27:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[12:27:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[12:27:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[12:27:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[12:27:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:23:53] This is snippy 4.6.0Show full stderr[21:23:53] This is snippy 4.6.0
[21:23:53] Written by Torsten Seemann
[21:23:53] Obtained from https://github.com/tseemann/snippy
[21:23:53] Detected operating system: linux
[21:23:53] Enabling bundled linux tools.
[21:23:53] Found bwa - /usr/local/bin/bwa
[21:23:53] Found bcftools - /usr/local/bin/bcftools
[21:23:53] Found samtools - /usr/local/bin/samtools
[21:23:53] Found java - /usr/local/bin/java
[21:23:53] Found snpEff - /usr/local/bin/snpEff
[21:23:53] Found samclip - /usr/local/bin/samclip
[21:23:53] Found seqtk - /usr/local/bin/seqtk
[21:23:53] Found parallel - /usr/local/bin/parallel
[21:23:53] Found freebayes - /usr/local/bin/freebayes
[21:23:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:23:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:23:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:23:53] Found vcfuniq - /usr/local/bin/vcfuniq
[21:23:53] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:23:53] Found gzip - /bin/gzip
[21:23:53] Found vt - /usr/local/bin/vt
[21:23:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:23:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:23:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:23:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:23:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:23:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:23:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:23:54] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:27:43] This is snippy 4.6.0Show full stderr[21:27:43] This is snippy 4.6.0
[21:27:43] Written by Torsten Seemann
[21:27:43] Obtained from https://github.com/tseemann/snippy
[21:27:43] Detected operating system: linux
[21:27:43] Enabling bundled linux tools.
[21:27:43] Found bwa - /usr/local/bin/bwa
[21:27:43] Found bcftools - /usr/local/bin/bcftools
[21:27:43] Found samtools - /usr/local/bin/samtools
[21:27:43] Found java - /usr/local/bin/java
[21:27:43] Found snpEff - /usr/local/bin/snpEff
[21:27:43] Found samclip - /usr/local/bin/samclip
[21:27:43] Found seqtk - /usr/local/bin/seqtk
[21:27:43] Found parallel - /usr/local/bin/parallel
[21:27:43] Found freebayes - /usr/local/bin/freebayes
[21:27:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:27:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:27:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:27:43] Found vcfuniq - /usr/local/bin/vcfuniq
[21:27:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:27:43] Found gzip - /bin/gzip
[21:27:43] Found vt - /usr/local/bin/vt
[21:27:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:27:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:27:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:27:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:27:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:27:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:27:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:27:44] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [21:27:50] This is snippy 4.6.0Show full stderr[21:27:50] This is snippy 4.6.0
[21:27:50] Written by Torsten Seemann
[21:27:50] Obtained from https://github.com/tseemann/snippy
[21:27:50] Detected operating system: linux
[21:27:50] Enabling bundled linux tools.
[21:27:50] Found bwa - /usr/local/bin/bwa
[21:27:50] Found bcftools - /usr/local/bin/bcftools
[21:27:50] Found samtools - /usr/local/bin/samtools
[21:27:50] Found java - /usr/local/bin/java
[21:27:50] Found snpEff - /usr/local/bin/snpEff
[21:27:50] Found samclip - /usr/local/bin/samclip
[21:27:50] Found seqtk - /usr/local/bin/seqtk
[21:27:50] Found parallel - /usr/local/bin/parallel
[21:27:50] Found freebayes - /usr/local/bin/freebayes
[21:27:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:27:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:27:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:27:50] Found vcfuniq - /usr/local/bin/vcfuniq
[21:27:50] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:27:50] Found gzip - /bin/gzip
[21:27:50] Found vt - /usr/local/bin/vt
[21:27:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:27:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:27:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:27:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:27:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:27:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:27:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:27:51] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:55:39] This is snippy 4.6.0Show full stderr[01:55:39] This is snippy 4.6.0
[01:55:39] Written by Torsten Seemann
[01:55:39] Obtained from https://github.com/tseemann/snippy
[01:55:39] Detected operating system: linux
[01:55:39] Enabling bundled linux tools.
[01:55:39] Found bwa - /usr/local/bin/bwa
[01:55:39] Found bcftools - /usr/local/bin/bcftools
[01:55:39] Found samtools - /usr/local/bin/samtools
[01:55:39] Found java - /usr/local/bin/java
[01:55:39] Found snpEff - /usr/local/bin/snpEff
[01:55:39] Found samclip - /usr/local/bin/samclip
[01:55:39] Found seqtk - /usr/local/bin/seqtk
[01:55:39] Found parallel - /usr/local/bin/parallel
[01:55:39] Found freebayes - /usr/local/bin/freebayes
[01:55:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:55:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:55:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:55:39] Found vcfuniq - /usr/local/bin/vcfuniq
[01:55:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:55:39] Found gzip - /bin/gzip
[01:55:39] Found vt - /usr/local/bin/vt
[01:55:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:55:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:55:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:55:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:55:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:55:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:55:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:55:40] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:58:22] This is snippy 4.6.0Show full stderr[01:58:22] This is snippy 4.6.0
[01:58:22] Written by Torsten Seemann
[01:58:22] Obtained from https://github.com/tseemann/snippy
[01:58:22] Detected operating system: linux
[01:58:22] Enabling bundled linux tools.
[01:58:22] Found bwa - /usr/local/bin/bwa
[01:58:22] Found bcftools - /usr/local/bin/bcftools
[01:58:22] Found samtools - /usr/local/bin/samtools
[01:58:22] Found java - /usr/local/bin/java
[01:58:23] Found snpEff - /usr/local/bin/snpEff
[01:58:23] Found samclip - /usr/local/bin/samclip
[01:58:23] Found seqtk - /usr/local/bin/seqtk
[01:58:23] Found parallel - /usr/local/bin/parallel
[01:58:23] Found freebayes - /usr/local/bin/freebayes
[01:58:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:58:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:58:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:58:23] Found vcfuniq - /usr/local/bin/vcfuniq
[01:58:23] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:58:23] Found gzip - /bin/gzip
[01:58:23] Found vt - /usr/local/bin/vt
[01:58:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:58:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:58:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:58:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:58:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:58:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:58:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:58:23] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [06:10:13] This is snippy 4.6.0Show full stderr[06:10:13] This is snippy 4.6.0
[06:10:13] Written by Torsten Seemann
[06:10:13] Obtained from https://github.com/tseemann/snippy
[06:10:13] Detected operating system: linux
[06:10:13] Enabling bundled linux tools.
[06:10:13] Found bwa - /usr/local/bin/bwa
[06:10:13] Found bcftools - /usr/local/bin/bcftools
[06:10:13] Found samtools - /usr/local/bin/samtools
[06:10:13] Found java - /usr/local/bin/java
[06:10:13] Found snpEff - /usr/local/bin/snpEff
[06:10:14] Found samclip - /usr/local/bin/samclip
[06:10:14] Found seqtk - /usr/local/bin/seqtk
[06:10:14] Found parallel - /usr/local/bin/parallel
[06:10:14] Found freebayes - /usr/local/bin/freebayes
[06:10:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[06:10:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[06:10:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[06:10:14] Found vcfuniq - /usr/local/bin/vcfuniq
[06:10:14] Found vcffirstheader - /usr/local/bin/vcffirstheader
[06:10:14] Found gzip - /bin/gzip
[06:10:14] Found vt - /usr/local/bin/vt
[06:10:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[06:10:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[06:10:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[06:10:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[06:10:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[06:10:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[06:10:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[06:10:15] Using reference: /corral4/main/objects/e/5/8/dataset_e58c24e1-626b-401e-a605-9dc03243b89b.dat
[06:10:15] Treating reference as 'genbank' format.
[06:10:15] Will use 1 CPU cores.
[06:10:15] Using read file: /corral4/main/objects/0/4/d/dataset_04d17ee1-81fe-40d8-912e-65330ca56649.dat
[06:10:15] Using read file: /corral4/main/objects/8/3/c/dataset_83c4b454-5c92-43f6-af36-3e60419df6bd.dat
[06:10:15] Creating folder: Trimmomatic_on_17EIW9_S21_L001_R1_001_fastq_gz__R1_paired_
[06:10:15] Changing working directory: Trimmomatic_on_17EIW9_S21_L001_R1_001_fastq_gz__R1_paired_
[06:10:15] Creating reference folder: reference
[06:10:15] Extracting FASTA and GFF from reference.
Use of uninitialized value in uc at /usr/local/bin/snippy line 206, <GEN0> line 84.
[06:10:15] Wrote 1 sequences to ref.fa
[06:10:15] Wrote 0 features to ref.gff
[06:10:15] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[06:10:15] Using BAM RG (Read Group) ID: Trimmomatic_on_17EIW9_S21_L001_R1_001_fastq_gz__R1_paired_
[06:10:15] Running: samtools faidx reference/ref.fa 2>> snps.log
[06:10:15] Error running command, check Trimmomatic_on_17EIW9_S21_L001_R1_001_fastq_gz__R1_paired_/snps.log |
| 1 | [02:09:28] This is snippy 4.6.0Show full stderr[02:09:28] This is snippy 4.6.0
[02:09:28] Written by Torsten Seemann
[02:09:28] Obtained from https://github.com/tseemann/snippy
[02:09:28] Detected operating system: linux
[02:09:28] Enabling bundled linux tools.
[02:09:28] Found bwa - /usr/local/bin/bwa
[02:09:28] Found bcftools - /usr/local/bin/bcftools
[02:09:28] Found samtools - /usr/local/bin/samtools
[02:09:28] Found java - /usr/local/bin/java
[02:09:28] Found snpEff - /usr/local/bin/snpEff
[02:09:28] Found samclip - /usr/local/bin/samclip
[02:09:28] Found seqtk - /usr/local/bin/seqtk
[02:09:28] Found parallel - /usr/local/bin/parallel
[02:09:28] Found freebayes - /usr/local/bin/freebayes
[02:09:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:09:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:09:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:09:28] Found vcfuniq - /usr/local/bin/vcfuniq
[02:09:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:09:28] Found gzip - /bin/gzip
[02:09:28] Found vt - /usr/local/bin/vt
[02:09:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:09:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:09:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:09:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:09:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:09:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:09:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:09:29] Using reference: /corral4/main/objects/b/8/f/dataset_b8fd84bc-39ea-4631-bcf7-cf2275682208.dat
[02:09:29] Treating reference as 'genbank' format.
[02:09:29] Will use 1 CPU cores.
[02:09:29] Using read file: /corral4/main/objects/d/1/9/dataset_d198d016-bd24-4ea3-a2cb-969dbc125b01.dat
[02:09:29] Using read file: /corral4/main/objects/2/9/c/dataset_29c0f420-3e0c-4496-a95c-04d629204009.dat
[02:09:29] Creating folder: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1
[02:09:29] Changing working directory: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1
[02:09:29] Creating reference folder: reference
[02:09:29] Extracting FASTA and GFF from reference.
[02:09:32] Wrote 1 sequences to ref.fa
[02:09:32] Wrote 5017 features to ref.gff
[02:09:32] Creating reference/snpeff.config
[02:09:32] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time.
[02:09:32] Using BAM RG (Read Group) ID: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1
[02:09:32] Running: samtools faidx reference/ref.fa 2>> snps.log
[02:09:32] Error running command, check Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1/snps.log |
| 1 | [07:42:58] This is snippy 4.6.0Show full stderr[07:42:58] This is snippy 4.6.0
[07:42:58] Written by Torsten Seemann
[07:42:58] Obtained from https://github.com/tseemann/snippy
[07:42:58] Detected operating system: linux
[07:42:58] Enabling bundled linux tools.
[07:42:58] Found bwa - /usr/local/bin/bwa
[07:42:58] Found bcftools - /usr/local/bin/bcftools
[07:42:58] Found samtools - /usr/local/bin/samtools
[07:42:58] Found java - /usr/local/bin/java
[07:42:58] Found snpEff - /usr/local/bin/snpEff
[07:42:58] Found samclip - /usr/local/bin/samclip
[07:42:58] Found seqtk - /usr/local/bin/seqtk
[07:42:58] Found parallel - /usr/local/bin/parallel
[07:42:58] Found freebayes - /usr/local/bin/freebayes
[07:42:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:42:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:42:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:42:58] Found vcfuniq - /usr/local/bin/vcfuniq
[07:42:58] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:42:58] Found gzip - /bin/gzip
[07:42:58] Found vt - /usr/local/bin/vt
[07:42:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:42:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:42:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:42:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:42:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:42:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:42:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:42:59] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [11:35:07] This is snippy 4.6.0Show full stderr[11:35:07] This is snippy 4.6.0
[11:35:07] Written by Torsten Seemann
[11:35:07] Obtained from https://github.com/tseemann/snippy
[11:35:07] Detected operating system: linux
[11:35:07] Enabling bundled linux tools.
[11:35:07] Found bwa - /usr/local/bin/bwa
[11:35:07] Found bcftools - /usr/local/bin/bcftools
[11:35:07] Found samtools - /usr/local/bin/samtools
[11:35:07] Found java - /usr/local/bin/java
[11:35:07] Found snpEff - /usr/local/bin/snpEff
[11:35:07] Found samclip - /usr/local/bin/samclip
[11:35:07] Found seqtk - /usr/local/bin/seqtk
[11:35:07] Found parallel - /usr/local/bin/parallel
[11:35:07] Found freebayes - /usr/local/bin/freebayes
[11:35:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[11:35:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[11:35:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[11:35:07] Found vcfuniq - /usr/local/bin/vcfuniq
[11:35:07] Found vcffirstheader - /usr/local/bin/vcffirstheader
[11:35:07] Found gzip - /bin/gzip
[11:35:07] Found vt - /usr/local/bin/vt
[11:35:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[11:35:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[11:35:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[11:35:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[11:35:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[11:35:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[11:35:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[11:35:08] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [11:35:49] This is snippy 4.6.0Show full stderr[11:35:49] This is snippy 4.6.0
[11:35:49] Written by Torsten Seemann
[11:35:49] Obtained from https://github.com/tseemann/snippy
[11:35:49] Detected operating system: linux
[11:35:49] Enabling bundled linux tools.
[11:35:49] Found bwa - /usr/local/bin/bwa
[11:35:49] Found bcftools - /usr/local/bin/bcftools
[11:35:49] Found samtools - /usr/local/bin/samtools
[11:35:49] Found java - /usr/local/bin/java
[11:35:49] Found snpEff - /usr/local/bin/snpEff
[11:35:49] Found samclip - /usr/local/bin/samclip
[11:35:49] Found seqtk - /usr/local/bin/seqtk
[11:35:49] Found parallel - /usr/local/bin/parallel
[11:35:49] Found freebayes - /usr/local/bin/freebayes
[11:35:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[11:35:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[11:35:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[11:35:49] Found vcfuniq - /usr/local/bin/vcfuniq
[11:35:49] Found vcffirstheader - /usr/local/bin/vcffirstheader
[11:35:49] Found gzip - /bin/gzip
[11:35:49] Found vt - /usr/local/bin/vt
[11:35:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[11:35:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[11:35:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[11:35:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[11:35:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[11:35:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[11:35:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[11:35:50] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [11:36:38] This is snippy 4.6.0Show full stderr[11:36:38] This is snippy 4.6.0
[11:36:38] Written by Torsten Seemann
[11:36:38] Obtained from https://github.com/tseemann/snippy
[11:36:38] Detected operating system: linux
[11:36:38] Enabling bundled linux tools.
[11:36:38] Found bwa - /usr/local/bin/bwa
[11:36:38] Found bcftools - /usr/local/bin/bcftools
[11:36:38] Found samtools - /usr/local/bin/samtools
[11:36:38] Found java - /usr/local/bin/java
[11:36:38] Found snpEff - /usr/local/bin/snpEff
[11:36:38] Found samclip - /usr/local/bin/samclip
[11:36:38] Found seqtk - /usr/local/bin/seqtk
[11:36:38] Found parallel - /usr/local/bin/parallel
[11:36:38] Found freebayes - /usr/local/bin/freebayes
[11:36:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[11:36:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[11:36:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[11:36:38] Found vcfuniq - /usr/local/bin/vcfuniq
[11:36:38] Found vcffirstheader - /usr/local/bin/vcffirstheader
[11:36:38] Found gzip - /bin/gzip
[11:36:38] Found vt - /usr/local/bin/vt
[11:36:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[11:36:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[11:36:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[11:36:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[11:36:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[11:36:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[11:36:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[11:36:39] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [11:37:20] This is snippy 4.6.0Show full stderr[11:37:20] This is snippy 4.6.0
[11:37:20] Written by Torsten Seemann
[11:37:20] Obtained from https://github.com/tseemann/snippy
[11:37:20] Detected operating system: linux
[11:37:20] Enabling bundled linux tools.
[11:37:20] Found bwa - /usr/local/bin/bwa
[11:37:20] Found bcftools - /usr/local/bin/bcftools
[11:37:20] Found samtools - /usr/local/bin/samtools
[11:37:20] Found java - /usr/local/bin/java
[11:37:20] Found snpEff - /usr/local/bin/snpEff
[11:37:20] Found samclip - /usr/local/bin/samclip
[11:37:20] Found seqtk - /usr/local/bin/seqtk
[11:37:20] Found parallel - /usr/local/bin/parallel
[11:37:20] Found freebayes - /usr/local/bin/freebayes
[11:37:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[11:37:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[11:37:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[11:37:20] Found vcfuniq - /usr/local/bin/vcfuniq
[11:37:20] Found vcffirstheader - /usr/local/bin/vcffirstheader
[11:37:20] Found gzip - /bin/gzip
[11:37:20] Found vt - /usr/local/bin/vt
[11:37:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[11:37:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[11:37:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[11:37:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[11:37:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[11:37:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[11:37:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[11:37:21] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [14:15:28] This is snippy 4.6.0Show full stderr[14:15:28] This is snippy 4.6.0
[14:15:28] Written by Torsten Seemann
[14:15:28] Obtained from https://github.com/tseemann/snippy
[14:15:28] Detected operating system: linux
[14:15:28] Enabling bundled linux tools.
[14:15:28] Found bwa - /usr/local/bin/bwa
[14:15:28] Found bcftools - /usr/local/bin/bcftools
[14:15:28] Found samtools - /usr/local/bin/samtools
[14:15:28] Found java - /usr/local/bin/java
[14:15:28] Found snpEff - /usr/local/bin/snpEff
[14:15:28] Found samclip - /usr/local/bin/samclip
[14:15:28] Found seqtk - /usr/local/bin/seqtk
[14:15:28] Found parallel - /usr/local/bin/parallel
[14:15:28] Found freebayes - /usr/local/bin/freebayes
[14:15:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[14:15:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[14:15:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[14:15:28] Found vcfuniq - /usr/local/bin/vcfuniq
[14:15:28] Found vcffirstheader - /usr/local/bin/vcffirstheader
[14:15:28] Found gzip - /bin/gzip
[14:15:28] Found vt - /usr/local/bin/vt
[14:15:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[14:15:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[14:15:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[14:15:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[14:15:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[14:15:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[14:15:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[14:15:29] Using reference: /corral4/main/objects/b/c/6/dataset_bc64c99a-098a-4a41-9acd-d60322a2c629.dat
[14:15:29] Treating reference as 'fasta' format.
[14:15:29] Will use 1 CPU cores.
[14:15:29] Using read file: /corral4/main/objects/c/1/4/dataset_c1497bab-6824-4297-86c0-caec26b178f0.dat
[14:15:29] Using read file: /corral4/main/objects/2/0/0/dataset_200e2f81-1b65-4350-90e3-3d01c6420d58.dat
[14:15:29] Creating folder: 317753_A2_1_trimmed_fastq_gz
[14:15:29] Changing working directory: 317753_A2_1_trimmed_fastq_gz
[14:15:29] Creating reference folder: reference
[14:15:29] Extracting FASTA and GFF from reference.
[14:15:29] Duplicate sequence PGD104247 in /corral4/main/objects/b/c/6/dataset_bc64c99a-098a-4a41-9acd-d60322a2c629.dat |
| 1 | [21:39:12] This is snippy 4.6.0Show full stderr[21:39:12] This is snippy 4.6.0
[21:39:12] Written by Torsten Seemann
[21:39:12] Obtained from https://github.com/tseemann/snippy
[21:39:12] Detected operating system: linux
[21:39:12] Enabling bundled linux tools.
[21:39:12] Found bwa - /usr/local/bin/bwa
[21:39:12] Found bcftools - /usr/local/bin/bcftools
[21:39:12] Found samtools - /usr/local/bin/samtools
[21:39:12] Found java - /usr/local/bin/java
[21:39:12] Found snpEff - /usr/local/bin/snpEff
[21:39:12] Found samclip - /usr/local/bin/samclip
[21:39:12] Found seqtk - /usr/local/bin/seqtk
[21:39:12] Found parallel - /usr/local/bin/parallel
[21:39:12] Found freebayes - /usr/local/bin/freebayes
[21:39:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[21:39:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[21:39:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[21:39:12] Found vcfuniq - /usr/local/bin/vcfuniq
[21:39:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[21:39:12] Found gzip - /bin/gzip
[21:39:12] Found vt - /usr/local/bin/vt
[21:39:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[21:39:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[21:39:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[21:39:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[21:39:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[21:39:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:39:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[21:39:14] Using reference: /corral4/main/objects/6/0/2/dataset_6023055f-9028-43b4-93e3-88a86498afa1.dat
[21:39:16] Treating reference as 'genbank' format.
[21:39:16] Will use 1 CPU cores.
[21:39:16] Using read file: /corral4/main/objects/a/5/3/dataset_a5387cee-8bf5-436d-a74c-21634876c586.dat
[21:39:16] Using read file: /corral4/main/objects/0/3/6/dataset_03698956-ef1e-40c3-9bed-675afa86f1c3.dat
[21:39:16] Creating folder: SRR29263914
[21:39:16] Changing working directory: SRR29263914
[21:39:16] Creating reference folder: reference
[21:39:17] Extracting FASTA and GFF from reference.
--------------------- WARNING ---------------------
MSG: Bad LOCUS name? Changing [NODE_1_length_657186_cov_100.680931657186] to 'unknown' and length to 'NODE_1_length_657186_cov_100.680931657186'
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Bad LOCUS name? Changing [NODE_2_length_636502_cov_103.943722636502] to 'unknown' and length to 'NODE_2_length_636502_cov_103.943722636502'
---------------------------------------------------
[21:39:17] Duplicate sequence unknown in /corral4/main/objects/6/0/2/dataset_6023055f-9028-43b4-93e3-88a86498afa1.dat |
| 1 | [22:01:43] This is snippy 4.6.0Show full stderr[22:01:43] This is snippy 4.6.0
[22:01:43] Written by Torsten Seemann
[22:01:43] Obtained from https://github.com/tseemann/snippy
[22:01:43] Detected operating system: linux
[22:01:43] Enabling bundled linux tools.
[22:01:43] Found bwa - /usr/local/bin/bwa
[22:01:43] Found bcftools - /usr/local/bin/bcftools
[22:01:43] Found samtools - /usr/local/bin/samtools
[22:01:43] Found java - /usr/local/bin/java
[22:01:43] Found snpEff - /usr/local/bin/snpEff
[22:01:43] Found samclip - /usr/local/bin/samclip
[22:01:43] Found seqtk - /usr/local/bin/seqtk
[22:01:43] Found parallel - /usr/local/bin/parallel
[22:01:43] Found freebayes - /usr/local/bin/freebayes
[22:01:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[22:01:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[22:01:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[22:01:43] Found vcfuniq - /usr/local/bin/vcfuniq
[22:01:43] Found vcffirstheader - /usr/local/bin/vcffirstheader
[22:01:43] Found gzip - /bin/gzip
[22:01:43] Found vt - /usr/local/bin/vt
[22:01:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[22:01:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[22:01:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[22:01:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[22:01:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[22:01:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[22:01:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[22:01:44] Using reference: /corral4/main/objects/9/c/a/dataset_9cabf3b6-e6d3-4dcd-8e07-292b26f608af.dat
[22:01:44] Treating reference as 'fasta' format.
[22:01:44] Will use 1 CPU cores.
[22:01:44] Using read file: /corral4/main/objects/1/d/7/dataset_1d7bb7d9-1fb9-4358-b904-2d372d1dc701.dat
[22:01:44] Using read file: /corral4/main/objects/6/4/0/dataset_6403a9a4-acfb-454f-b397-c408c55b4140.dat
[22:01:44] Creating folder: SRR12131097
[22:01:44] Changing working directory: SRR12131097
[22:01:44] Creating reference folder: reference
[22:01:44] Extracting FASTA and GFF from reference.
[22:01:45] Wrote 4 sequences to ref.fa
[22:01:45] Wrote 0 features to ref.gff
[22:01:45] Freebayes will process 1 chunks of 6687074 bp, 1 chunks at a time.
[22:01:45] Using BAM RG (Read Group) ID: SRR12131097
[22:01:45] Running: samtools faidx reference/ref.fa 2>> snps.log
[22:01:45] Running: bwa index reference/ref.fa 2>> snps.log
[22:01:52] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[22:01:52] Running: ln -sf reference/ref.fa . 2>> snps.log
[22:01:52] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[22:01:53] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[22:01:53] Running: bwa mem -Y -M -R '@RG\tID:SRR12131097\tSM:SRR12131097' -t 1 reference/ref.fa /corral4/main/objects/1/d/7/dataset_1d7bb7d9-1fb9-4358-b904-2d372d1dc701.dat /corral4/main/objects/6/4/0/dataset_6403a9a4-acfb-454f-b397-c408c55b4140.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/225/73225392/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/225/73225392/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/225/73225392/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 4 sequences in reference/ref.fa.fai
[M::pro |
| 1 | [23:59:17] This is snippy 4.6.0Show full stderr[23:59:17] This is snippy 4.6.0
[23:59:17] Written by Torsten Seemann
[23:59:17] Obtained from https://github.com/tseemann/snippy
[23:59:17] Detected operating system: linux
[23:59:17] Enabling bundled linux tools.
[23:59:17] Found bwa - /usr/local/bin/bwa
[23:59:17] Found bcftools - /usr/local/bin/bcftools
[23:59:17] Found samtools - /usr/local/bin/samtools
[23:59:17] Found java - /usr/local/bin/java
[23:59:17] Found snpEff - /usr/local/bin/snpEff
[23:59:17] Found samclip - /usr/local/bin/samclip
[23:59:17] Found seqtk - /usr/local/bin/seqtk
[23:59:17] Found parallel - /usr/local/bin/parallel
[23:59:17] Found freebayes - /usr/local/bin/freebayes
[23:59:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:59:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:59:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:59:17] Found vcfuniq - /usr/local/bin/vcfuniq
[23:59:17] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:59:17] Found gzip - /bin/gzip
[23:59:17] Found vt - /usr/local/bin/vt
[23:59:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:59:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:59:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:59:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:59:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:59:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:59:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:59:17] Using reference: /corral4/main/objects/2/e/1/dataset_2e11e81e-1139-4b27-a8be-8b1907183159.dat
[23:59:18] Treating reference as 'genbank' format.
[23:59:18] Will use 1 CPU cores.
[23:59:18] Using read file: /corral4/main/objects/e/d/2/dataset_ed2636a4-201d-496a-a51b-89a76b9503c8.dat
[23:59:18] Using read file: /corral4/main/objects/8/3/6/dataset_836031cd-336f-451b-af07-41dd1df77396.dat
[23:59:18] Creating folder: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1
[23:59:18] Changing working directory: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1
[23:59:18] Creating reference folder: reference
[23:59:18] Extracting FASTA and GFF from reference.
[23:59:31] Wrote 4901 sequences to ref.fa
[23:59:31] Wrote 4901 features to ref.gff
[23:59:31] Creating reference/snpeff.config
[23:59:31] Freebayes will process 1 chunks of 1944614 bp, 1 chunks at a time.
[23:59:31] Using BAM RG (Read Group) ID: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1
[23:59:31] Running: samtools faidx reference/ref.fa 2>> snps.log
[23:59:31] Running: bwa index reference/ref.fa 2>> snps.log
[23:59:32] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[23:59:32] Running: ln -sf reference/ref.fa . 2>> snps.log
[23:59:32] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[23:59:32] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[23:59:32] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[23:59:41] Error running command, check Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1/snps.log |
| 1 | [00:12:59] This is snippy 4.6.0Show full stderr[00:12:59] This is snippy 4.6.0
[00:12:59] Written by Torsten Seemann
[00:12:59] Obtained from https://github.com/tseemann/snippy
[00:12:59] Detected operating system: linux
[00:12:59] Enabling bundled linux tools.
[00:12:59] Found bwa - /usr/local/bin/bwa
[00:12:59] Found bcftools - /usr/local/bin/bcftools
[00:12:59] Found samtools - /usr/local/bin/samtools
[00:12:59] Found java - /usr/local/bin/java
[00:12:59] Found snpEff - /usr/local/bin/snpEff
[00:12:59] Found samclip - /usr/local/bin/samclip
[00:12:59] Found seqtk - /usr/local/bin/seqtk
[00:12:59] Found parallel - /usr/local/bin/parallel
[00:12:59] Found freebayes - /usr/local/bin/freebayes
[00:12:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:12:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:12:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:12:59] Found vcfuniq - /usr/local/bin/vcfuniq
[00:12:59] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:12:59] Found gzip - /bin/gzip
[00:12:59] Found vt - /usr/local/bin/vt
[00:12:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:12:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:13:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:13:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:13:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:13:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:13:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:13:00] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:18:16] This is snippy 4.6.0Show full stderr[00:18:16] This is snippy 4.6.0
[00:18:16] Written by Torsten Seemann
[00:18:16] Obtained from https://github.com/tseemann/snippy
[00:18:16] Detected operating system: linux
[00:18:16] Enabling bundled linux tools.
[00:18:16] Found bwa - /usr/local/bin/bwa
[00:18:16] Found bcftools - /usr/local/bin/bcftools
[00:18:16] Found samtools - /usr/local/bin/samtools
[00:18:16] Found java - /usr/local/bin/java
[00:18:16] Found snpEff - /usr/local/bin/snpEff
[00:18:16] Found samclip - /usr/local/bin/samclip
[00:18:16] Found seqtk - /usr/local/bin/seqtk
[00:18:16] Found parallel - /usr/local/bin/parallel
[00:18:16] Found freebayes - /usr/local/bin/freebayes
[00:18:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:18:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:18:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:18:16] Found vcfuniq - /usr/local/bin/vcfuniq
[00:18:16] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:18:16] Found gzip - /bin/gzip
[00:18:16] Found vt - /usr/local/bin/vt
[00:18:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:18:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:18:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:18:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:18:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:18:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:18:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:18:17] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:20:15] This is snippy 4.6.0Show full stderr[00:20:15] This is snippy 4.6.0
[00:20:15] Written by Torsten Seemann
[00:20:15] Obtained from https://github.com/tseemann/snippy
[00:20:15] Detected operating system: linux
[00:20:15] Enabling bundled linux tools.
[00:20:15] Found bwa - /usr/local/bin/bwa
[00:20:15] Found bcftools - /usr/local/bin/bcftools
[00:20:15] Found samtools - /usr/local/bin/samtools
[00:20:15] Found java - /usr/local/bin/java
[00:20:15] Found snpEff - /usr/local/bin/snpEff
[00:20:15] Found samclip - /usr/local/bin/samclip
[00:20:15] Found seqtk - /usr/local/bin/seqtk
[00:20:15] Found parallel - /usr/local/bin/parallel
[00:20:15] Found freebayes - /usr/local/bin/freebayes
[00:20:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:20:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:20:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:20:15] Found vcfuniq - /usr/local/bin/vcfuniq
[00:20:15] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:20:15] Found gzip - /bin/gzip
[00:20:15] Found vt - /usr/local/bin/vt
[00:20:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:20:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:20:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:20:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:20:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:20:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:20:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:20:16] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:45:11] This is snippy 4.6.0Show full stderr[00:45:11] This is snippy 4.6.0
[00:45:11] Written by Torsten Seemann
[00:45:11] Obtained from https://github.com/tseemann/snippy
[00:45:11] Detected operating system: linux
[00:45:11] Enabling bundled linux tools.
[00:45:11] Found bwa - /usr/local/bin/bwa
[00:45:11] Found bcftools - /usr/local/bin/bcftools
[00:45:11] Found samtools - /usr/local/bin/samtools
[00:45:11] Found java - /usr/local/bin/java
[00:45:11] Found snpEff - /usr/local/bin/snpEff
[00:45:11] Found samclip - /usr/local/bin/samclip
[00:45:11] Found seqtk - /usr/local/bin/seqtk
[00:45:11] Found parallel - /usr/local/bin/parallel
[00:45:11] Found freebayes - /usr/local/bin/freebayes
[00:45:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:45:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:45:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:45:11] Found vcfuniq - /usr/local/bin/vcfuniq
[00:45:11] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:45:11] Found gzip - /bin/gzip
[00:45:11] Found vt - /usr/local/bin/vt
[00:45:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:45:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:45:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:45:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:45:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:45:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:45:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:45:12] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [00:55:40] This is snippy 4.6.0Show full stderr[00:55:40] This is snippy 4.6.0
[00:55:40] Written by Torsten Seemann
[00:55:40] Obtained from https://github.com/tseemann/snippy
[00:55:40] Detected operating system: linux
[00:55:40] Enabling bundled linux tools.
[00:55:40] Found bwa - /usr/local/bin/bwa
[00:55:40] Found bcftools - /usr/local/bin/bcftools
[00:55:40] Found samtools - /usr/local/bin/samtools
[00:55:40] Found java - /usr/local/bin/java
[00:55:40] Found snpEff - /usr/local/bin/snpEff
[00:55:40] Found samclip - /usr/local/bin/samclip
[00:55:40] Found seqtk - /usr/local/bin/seqtk
[00:55:40] Found parallel - /usr/local/bin/parallel
[00:55:40] Found freebayes - /usr/local/bin/freebayes
[00:55:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[00:55:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[00:55:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[00:55:40] Found vcfuniq - /usr/local/bin/vcfuniq
[00:55:40] Found vcffirstheader - /usr/local/bin/vcffirstheader
[00:55:40] Found gzip - /bin/gzip
[00:55:40] Found vt - /usr/local/bin/vt
[00:55:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[00:55:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[00:55:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[00:55:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[00:55:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[00:55:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[00:55:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[00:55:42] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:04:46] This is snippy 4.6.0Show full stderr[01:04:46] This is snippy 4.6.0
[01:04:46] Written by Torsten Seemann
[01:04:46] Obtained from https://github.com/tseemann/snippy
[01:04:46] Detected operating system: linux
[01:04:46] Enabling bundled linux tools.
[01:04:46] Found bwa - /usr/local/bin/bwa
[01:04:46] Found bcftools - /usr/local/bin/bcftools
[01:04:46] Found samtools - /usr/local/bin/samtools
[01:04:46] Found java - /usr/local/bin/java
[01:04:46] Found snpEff - /usr/local/bin/snpEff
[01:04:46] Found samclip - /usr/local/bin/samclip
[01:04:46] Found seqtk - /usr/local/bin/seqtk
[01:04:46] Found parallel - /usr/local/bin/parallel
[01:04:46] Found freebayes - /usr/local/bin/freebayes
[01:04:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:04:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:04:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:04:46] Found vcfuniq - /usr/local/bin/vcfuniq
[01:04:46] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:04:46] Found gzip - /bin/gzip
[01:04:46] Found vt - /usr/local/bin/vt
[01:04:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:04:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:04:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:04:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:04:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:04:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:04:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:04:48] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:08:19] This is snippy 4.6.0Show full stderr[01:08:19] This is snippy 4.6.0
[01:08:19] Written by Torsten Seemann
[01:08:19] Obtained from https://github.com/tseemann/snippy
[01:08:19] Detected operating system: linux
[01:08:19] Enabling bundled linux tools.
[01:08:19] Found bwa - /usr/local/bin/bwa
[01:08:19] Found bcftools - /usr/local/bin/bcftools
[01:08:19] Found samtools - /usr/local/bin/samtools
[01:08:19] Found java - /usr/local/bin/java
[01:08:19] Found snpEff - /usr/local/bin/snpEff
[01:08:19] Found samclip - /usr/local/bin/samclip
[01:08:19] Found seqtk - /usr/local/bin/seqtk
[01:08:19] Found parallel - /usr/local/bin/parallel
[01:08:19] Found freebayes - /usr/local/bin/freebayes
[01:08:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:08:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:08:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:08:19] Found vcfuniq - /usr/local/bin/vcfuniq
[01:08:19] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:08:19] Found gzip - /bin/gzip
[01:08:19] Found vt - /usr/local/bin/vt
[01:08:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:08:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:08:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:08:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:08:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:08:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:08:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:08:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:12:29] This is snippy 4.6.0Show full stderr[01:12:29] This is snippy 4.6.0
[01:12:29] Written by Torsten Seemann
[01:12:29] Obtained from https://github.com/tseemann/snippy
[01:12:29] Detected operating system: linux
[01:12:29] Enabling bundled linux tools.
[01:12:29] Found bwa - /usr/local/bin/bwa
[01:12:29] Found bcftools - /usr/local/bin/bcftools
[01:12:29] Found samtools - /usr/local/bin/samtools
[01:12:29] Found java - /usr/local/bin/java
[01:12:29] Found snpEff - /usr/local/bin/snpEff
[01:12:29] Found samclip - /usr/local/bin/samclip
[01:12:29] Found seqtk - /usr/local/bin/seqtk
[01:12:29] Found parallel - /usr/local/bin/parallel
[01:12:29] Found freebayes - /usr/local/bin/freebayes
[01:12:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:12:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:12:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:12:29] Found vcfuniq - /usr/local/bin/vcfuniq
[01:12:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:12:29] Found gzip - /bin/gzip
[01:12:29] Found vt - /usr/local/bin/vt
[01:12:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:12:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:12:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:12:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:12:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:12:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:12:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:12:36] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [01:35:09] This is snippy 4.6.0Show full stderr[01:35:09] This is snippy 4.6.0
[01:35:09] Written by Torsten Seemann
[01:35:09] Obtained from https://github.com/tseemann/snippy
[01:35:09] Detected operating system: linux
[01:35:09] Enabling bundled linux tools.
[01:35:09] Found bwa - /usr/local/bin/bwa
[01:35:09] Found bcftools - /usr/local/bin/bcftools
[01:35:09] Found samtools - /usr/local/bin/samtools
[01:35:09] Found java - /usr/local/bin/java
[01:35:09] Found snpEff - /usr/local/bin/snpEff
[01:35:09] Found samclip - /usr/local/bin/samclip
[01:35:09] Found seqtk - /usr/local/bin/seqtk
[01:35:09] Found parallel - /usr/local/bin/parallel
[01:35:09] Found freebayes - /usr/local/bin/freebayes
[01:35:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:35:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:35:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:35:09] Found vcfuniq - /usr/local/bin/vcfuniq
[01:35:09] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:35:10] Found gzip - /bin/gzip
[01:35:10] Found vt - /usr/local/bin/vt
[01:35:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:35:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:35:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:35:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:35:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:35:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:35:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:35:11] Using reference: /corral4/main/objects/9/e/0/dataset_9e02d4cd-cefb-4d60-bdfe-8d8d5dc517e2.dat
[01:35:11] Treating reference as 'genbank' format.
[01:35:11] Will use 1 CPU cores.
[01:35:11] Using read file: /corral4/main/objects/0/6/d/dataset_06ddbb48-7021-4b41-9eef-763850e97837.dat
[01:35:11] Creating folder: SPAdes_on_dataset_11_and_12_and_collection_9__Contigs
[01:35:11] Changing working directory: SPAdes_on_dataset_11_and_12_and_collection_9__Contigs
[01:35:11] Creating reference folder: reference
[01:35:11] Extracting FASTA and GFF from reference.
--------------------- WARNING ---------------------
MSG: Bad LOCUS name? Changing [NODE_1_length_657186_cov_83.784211657186] to 'unknown' and length to 'NODE_1_length_657186_cov_83.784211657186'
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Bad LOCUS name? Changing [NODE_2_length_642178_cov_95.522608642178] to 'unknown' and length to 'NODE_2_length_642178_cov_95.522608642178'
---------------------------------------------------
[01:35:12] Duplicate sequence unknown in /corral4/main/objects/9/e/0/dataset_9e02d4cd-cefb-4d60-bdfe-8d8d5dc517e2.dat |
| 1 | [01:41:29] This is snippy 4.6.0Show full stderr[01:41:29] This is snippy 4.6.0
[01:41:29] Written by Torsten Seemann
[01:41:29] Obtained from https://github.com/tseemann/snippy
[01:41:29] Detected operating system: linux
[01:41:29] Enabling bundled linux tools.
[01:41:29] Found bwa - /usr/local/bin/bwa
[01:41:29] Found bcftools - /usr/local/bin/bcftools
[01:41:29] Found samtools - /usr/local/bin/samtools
[01:41:29] Found java - /usr/local/bin/java
[01:41:29] Found snpEff - /usr/local/bin/snpEff
[01:41:29] Found samclip - /usr/local/bin/samclip
[01:41:29] Found seqtk - /usr/local/bin/seqtk
[01:41:29] Found parallel - /usr/local/bin/parallel
[01:41:29] Found freebayes - /usr/local/bin/freebayes
[01:41:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:41:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:41:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:41:29] Found vcfuniq - /usr/local/bin/vcfuniq
[01:41:29] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:41:29] Found gzip - /bin/gzip
[01:41:29] Found vt - /usr/local/bin/vt
[01:41:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:41:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:41:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:41:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:41:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:41:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:41:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:41:30] Using reference: /corral4/main/objects/f/b/5/dataset_fb57894d-62c4-4c95-aa14-2565ed9bd238.dat
[01:41:30] Treating reference as 'genbank' format.
[01:41:30] Will use 1 CPU cores.
[01:41:30] Using read file: /corral4/main/objects/4/8/3/dataset_4836aced-4bf9-4447-8ad6-c801870ffaae.dat
[01:41:30] Using read file: /corral4/main/objects/5/a/4/dataset_5a409afa-8107-4217-bc19-eb4adc63ad1e.dat
[01:41:30] Creating folder: SRR29263912
[01:41:30] Changing working directory: SRR29263912
[01:41:30] Creating reference folder: reference
[01:41:30] Extracting FASTA and GFF from reference.
--------------------- WARNING ---------------------
MSG: Bad LOCUS name? Changing [NODE_1_length_657186_cov_100.680931657186] to 'unknown' and length to 'NODE_1_length_657186_cov_100.680931657186'
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Bad LOCUS name? Changing [NODE_2_length_642180_cov_109.339456642180] to 'unknown' and length to 'NODE_2_length_642180_cov_109.339456642180'
---------------------------------------------------
[01:41:31] Duplicate sequence unknown in /corral4/main/objects/f/b/5/dataset_fb57894d-62c4-4c95-aa14-2565ed9bd238.dat |
| 1 | [01:56:36] This is snippy 4.6.0Show full stderr[01:56:36] This is snippy 4.6.0
[01:56:36] Written by Torsten Seemann
[01:56:36] Obtained from https://github.com/tseemann/snippy
[01:56:36] Detected operating system: linux
[01:56:36] Enabling bundled linux tools.
[01:56:36] Found bwa - /usr/local/bin/bwa
[01:56:36] Found bcftools - /usr/local/bin/bcftools
[01:56:37] Found samtools - /usr/local/bin/samtools
[01:56:37] Found java - /usr/local/bin/java
[01:56:37] Found snpEff - /usr/local/bin/snpEff
[01:56:37] Found samclip - /usr/local/bin/samclip
[01:56:37] Found seqtk - /usr/local/bin/seqtk
[01:56:37] Found parallel - /usr/local/bin/parallel
[01:56:37] Found freebayes - /usr/local/bin/freebayes
[01:56:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[01:56:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[01:56:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[01:56:37] Found vcfuniq - /usr/local/bin/vcfuniq
[01:56:37] Found vcffirstheader - /usr/local/bin/vcffirstheader
[01:56:37] Found gzip - /bin/gzip
[01:56:37] Found vt - /usr/local/bin/vt
[01:56:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[01:56:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[01:56:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[01:56:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[01:56:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[01:56:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[01:56:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[01:56:38] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:59:12] This is snippy 4.6.0Show full stderr[03:59:12] This is snippy 4.6.0
[03:59:12] Written by Torsten Seemann
[03:59:12] Obtained from https://github.com/tseemann/snippy
[03:59:12] Detected operating system: linux
[03:59:12] Enabling bundled linux tools.
[03:59:12] Found bwa - /usr/local/bin/bwa
[03:59:12] Found bcftools - /usr/local/bin/bcftools
[03:59:12] Found samtools - /usr/local/bin/samtools
[03:59:12] Found java - /usr/local/bin/java
[03:59:12] Found snpEff - /usr/local/bin/snpEff
[03:59:12] Found samclip - /usr/local/bin/samclip
[03:59:12] Found seqtk - /usr/local/bin/seqtk
[03:59:12] Found parallel - /usr/local/bin/parallel
[03:59:12] Found freebayes - /usr/local/bin/freebayes
[03:59:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:59:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:59:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:59:12] Found vcfuniq - /usr/local/bin/vcfuniq
[03:59:12] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:59:12] Found gzip - /bin/gzip
[03:59:12] Found vt - /usr/local/bin/vt
[03:59:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:59:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:59:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:59:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:59:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:59:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:59:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:59:13] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:02:18] This is snippy 4.6.0Show full stderr[05:02:18] This is snippy 4.6.0
[05:02:18] Written by Torsten Seemann
[05:02:18] Obtained from https://github.com/tseemann/snippy
[05:02:18] Detected operating system: linux
[05:02:18] Enabling bundled linux tools.
[05:02:18] Found bwa - /usr/local/bin/bwa
[05:02:18] Found bcftools - /usr/local/bin/bcftools
[05:02:18] Found samtools - /usr/local/bin/samtools
[05:02:18] Found java - /usr/local/bin/java
[05:02:18] Found snpEff - /usr/local/bin/snpEff
[05:02:18] Found samclip - /usr/local/bin/samclip
[05:02:18] Found seqtk - /usr/local/bin/seqtk
[05:02:18] Found parallel - /usr/local/bin/parallel
[05:02:18] Found freebayes - /usr/local/bin/freebayes
[05:02:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:02:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:02:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:02:18] Found vcfuniq - /usr/local/bin/vcfuniq
[05:02:18] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:02:18] Found gzip - /bin/gzip
[05:02:18] Found vt - /usr/local/bin/vt
[05:02:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:02:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:02:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:02:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:02:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:02:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:02:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:02:20] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:04:54] This is snippy 4.6.0Show full stderr[05:04:54] This is snippy 4.6.0
[05:04:54] Written by Torsten Seemann
[05:04:54] Obtained from https://github.com/tseemann/snippy
[05:04:54] Detected operating system: linux
[05:04:54] Enabling bundled linux tools.
[05:04:54] Found bwa - /usr/local/bin/bwa
[05:04:54] Found bcftools - /usr/local/bin/bcftools
[05:04:54] Found samtools - /usr/local/bin/samtools
[05:04:54] Found java - /usr/local/bin/java
[05:04:55] Found snpEff - /usr/local/bin/snpEff
[05:04:55] Found samclip - /usr/local/bin/samclip
[05:04:55] Found seqtk - /usr/local/bin/seqtk
[05:04:55] Found parallel - /usr/local/bin/parallel
[05:04:55] Found freebayes - /usr/local/bin/freebayes
[05:04:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:04:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:04:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:04:55] Found vcfuniq - /usr/local/bin/vcfuniq
[05:04:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:04:55] Found gzip - /bin/gzip
[05:04:55] Found vt - /usr/local/bin/vt
[05:04:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:04:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:04:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:04:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:04:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:04:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:04:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:04:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [05:37:33] This is snippy 4.6.0Show full stderr[05:37:33] This is snippy 4.6.0
[05:37:33] Written by Torsten Seemann
[05:37:33] Obtained from https://github.com/tseemann/snippy
[05:37:33] Detected operating system: linux
[05:37:33] Enabling bundled linux tools.
[05:37:33] Found bwa - /usr/local/bin/bwa
[05:37:33] Found bcftools - /usr/local/bin/bcftools
[05:37:33] Found samtools - /usr/local/bin/samtools
[05:37:33] Found java - /usr/local/bin/java
[05:37:33] Found snpEff - /usr/local/bin/snpEff
[05:37:33] Found samclip - /usr/local/bin/samclip
[05:37:33] Found seqtk - /usr/local/bin/seqtk
[05:37:33] Found parallel - /usr/local/bin/parallel
[05:37:33] Found freebayes - /usr/local/bin/freebayes
[05:37:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[05:37:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[05:37:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[05:37:33] Found vcfuniq - /usr/local/bin/vcfuniq
[05:37:33] Found vcffirstheader - /usr/local/bin/vcffirstheader
[05:37:33] Found gzip - /bin/gzip
[05:37:33] Found vt - /usr/local/bin/vt
[05:37:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[05:37:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[05:37:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[05:37:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[05:37:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[05:37:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[05:37:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[05:37:34] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [07:44:32] This is snippy 4.6.0Show full stderr[07:44:32] This is snippy 4.6.0
[07:44:32] Written by Torsten Seemann
[07:44:32] Obtained from https://github.com/tseemann/snippy
[07:44:32] Detected operating system: linux
[07:44:32] Enabling bundled linux tools.
[07:44:32] Found bwa - /usr/local/bin/bwa
[07:44:32] Found bcftools - /usr/local/bin/bcftools
[07:44:32] Found samtools - /usr/local/bin/samtools
[07:44:32] Found java - /usr/local/bin/java
[07:44:32] Found snpEff - /usr/local/bin/snpEff
[07:44:32] Found samclip - /usr/local/bin/samclip
[07:44:32] Found seqtk - /usr/local/bin/seqtk
[07:44:32] Found parallel - /usr/local/bin/parallel
[07:44:32] Found freebayes - /usr/local/bin/freebayes
[07:44:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[07:44:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[07:44:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[07:44:32] Found vcfuniq - /usr/local/bin/vcfuniq
[07:44:32] Found vcffirstheader - /usr/local/bin/vcffirstheader
[07:44:32] Found gzip - /bin/gzip
[07:44:32] Found vt - /usr/local/bin/vt
[07:44:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[07:44:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[07:44:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[07:44:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[07:44:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[07:44:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[07:44:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[07:44:33] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [23:17:57] This is snippy 4.6.0Show full stderr[23:17:57] This is snippy 4.6.0
[23:17:57] Written by Torsten Seemann
[23:17:57] Obtained from https://github.com/tseemann/snippy
[23:17:57] Detected operating system: linux
[23:17:57] Enabling bundled linux tools.
[23:17:57] Found bwa - /usr/local/bin/bwa
[23:17:57] Found bcftools - /usr/local/bin/bcftools
[23:17:57] Found samtools - /usr/local/bin/samtools
[23:17:57] Found java - /usr/local/bin/java
[23:17:57] Found snpEff - /usr/local/bin/snpEff
[23:17:57] Found samclip - /usr/local/bin/samclip
[23:17:57] Found seqtk - /usr/local/bin/seqtk
[23:17:57] Found parallel - /usr/local/bin/parallel
[23:17:57] Found freebayes - /usr/local/bin/freebayes
[23:17:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[23:17:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[23:17:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[23:17:57] Found vcfuniq - /usr/local/bin/vcfuniq
[23:17:57] Found vcffirstheader - /usr/local/bin/vcffirstheader
[23:17:57] Found gzip - /bin/gzip
[23:17:57] Found vt - /usr/local/bin/vt
[23:17:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[23:17:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[23:17:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[23:17:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[23:17:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[23:17:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[23:17:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[23:17:58] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:33:06] This is snippy 4.6.0Show full stderr[02:33:06] This is snippy 4.6.0
[02:33:06] Written by Torsten Seemann
[02:33:06] Obtained from https://github.com/tseemann/snippy
[02:33:06] Detected operating system: linux
[02:33:06] Enabling bundled linux tools.
[02:33:06] Found bwa - /usr/local/bin/bwa
[02:33:06] Found bcftools - /usr/local/bin/bcftools
[02:33:06] Found samtools - /usr/local/bin/samtools
[02:33:06] Found java - /usr/local/bin/java
[02:33:06] Found snpEff - /usr/local/bin/snpEff
[02:33:06] Found samclip - /usr/local/bin/samclip
[02:33:06] Found seqtk - /usr/local/bin/seqtk
[02:33:06] Found parallel - /usr/local/bin/parallel
[02:33:06] Found freebayes - /usr/local/bin/freebayes
[02:33:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:33:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:33:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:33:06] Found vcfuniq - /usr/local/bin/vcfuniq
[02:33:06] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:33:06] Found gzip - /bin/gzip
[02:33:06] Found vt - /usr/local/bin/vt
[02:33:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:33:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:33:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:33:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:33:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:33:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:33:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:33:07] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [02:45:55] This is snippy 4.6.0Show full stderr[02:45:55] This is snippy 4.6.0
[02:45:55] Written by Torsten Seemann
[02:45:55] Obtained from https://github.com/tseemann/snippy
[02:45:55] Detected operating system: linux
[02:45:55] Enabling bundled linux tools.
[02:45:55] Found bwa - /usr/local/bin/bwa
[02:45:55] Found bcftools - /usr/local/bin/bcftools
[02:45:55] Found samtools - /usr/local/bin/samtools
[02:45:55] Found java - /usr/local/bin/java
[02:45:55] Found snpEff - /usr/local/bin/snpEff
[02:45:55] Found samclip - /usr/local/bin/samclip
[02:45:55] Found seqtk - /usr/local/bin/seqtk
[02:45:55] Found parallel - /usr/local/bin/parallel
[02:45:55] Found freebayes - /usr/local/bin/freebayes
[02:45:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[02:45:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[02:45:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[02:45:55] Found vcfuniq - /usr/local/bin/vcfuniq
[02:45:55] Found vcffirstheader - /usr/local/bin/vcffirstheader
[02:45:55] Found gzip - /bin/gzip
[02:45:55] Found vt - /usr/local/bin/vt
[02:45:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[02:45:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[02:45:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[02:45:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[02:45:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[02:45:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[02:45:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[02:45:56] Please supply a reference FASTA/GBK/EMBL file with --reference |
| 1 | [03:28:39] This is snippy 4.6.0Show full stderr[03:28:39] This is snippy 4.6.0
[03:28:39] Written by Torsten Seemann
[03:28:39] Obtained from https://github.com/tseemann/snippy
[03:28:39] Detected operating system: linux
[03:28:39] Enabling bundled linux tools.
[03:28:39] Found bwa - /usr/local/bin/bwa
[03:28:39] Found bcftools - /usr/local/bin/bcftools
[03:28:39] Found samtools - /usr/local/bin/samtools
[03:28:39] Found java - /usr/local/bin/java
[03:28:39] Found snpEff - /usr/local/bin/snpEff
[03:28:39] Found samclip - /usr/local/bin/samclip
[03:28:39] Found seqtk - /usr/local/bin/seqtk
[03:28:39] Found parallel - /usr/local/bin/parallel
[03:28:39] Found freebayes - /usr/local/bin/freebayes
[03:28:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel
[03:28:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py
[03:28:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort
[03:28:39] Found vcfuniq - /usr/local/bin/vcfuniq
[03:28:39] Found vcffirstheader - /usr/local/bin/vcffirstheader
[03:28:39] Found gzip - /bin/gzip
[03:28:39] Found vt - /usr/local/bin/vt
[03:28:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab
[03:28:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report
[03:28:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13
[03:28:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13
[03:28:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2
[03:28:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[03:28:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[03:28:40] Please supply a reference FASTA/GBK/EMBL file with --reference |